First launching

Aditya Wibawa Sakti 2 years ago
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# Computational Molecular and Material Design Environment (CMMDE)
## Introduction
This software is developed for decreasing the barrier in using popular open-source computational chemistry software. Currently, CMMDE can use the following software:
1. [Orca](https://orcaforum.kofo.mpg.de/app.php/portal)
2. [DFTB+](https://dftbplus.org/)
3. [GROMACS](https://manual.gromacs.org/current/download.html)
4. [DOCK6](https://dock.compbio.ucsf.edu/DOCK_6/index.htm)
5. [DCDFTBMD](http://www.chem.waseda.ac.jp/dcdftbmd/?lang=en)
6. [Quantum Espresso](https://www.quantum-espresso.org/)
7. [xTB via Orca](https://github.com/grimme-lab/xtb)
## Installation
1. Cloning the repository:
```bash
git clone https://github.com/aditchemist/CMMDE
```
2. Change directory to CMMDE:
```bash
cd CMMDE
```
3. Install the code:
```bash
chmod +x install.sh
./install.sh
```

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#!/usr/bin/env python3
import sys
import os
import argparse
from cmmde_orca import orca
from cmmde_dcdftb import dcdftb
from cmmde_dock import readpdb, splitpdb, addH, addcharge, sphgen, showsphere, gridgen, rigiddock,flexdock, translig, sdf2xyz, multiopt, checkopt, multiflexdock
from cmmde_mdpro import proprep, ligprep
from cmmde_dftb import poscar2gen, vasp2gen, dftb
from cmmde_qe import qe
from cmmde_nw import nwchem
import time
parser = argparse.ArgumentParser(description='Computational Molecular & Material Design Interface')
# Input Geometri, tanpa ini perhitungan tidak akan berjalan.
parser.add_argument('-i','--input',type=str,default='geom.xyz',help='Input geometri dalam koordinat Cartesian')
parser.add_argument('-cons','--constraints',type=str,default='None',help='Membekukan ikatan, sudut ikatan, dan sebagainya selama proses optimasi geometri. Periksa manual Orca 5.0 lebih lanjut mengenai ini.')
# Informasi muatan dan multiplisitas spin molekul.
parser.add_argument('-c','--charge',type=int,default=0, help='Muatan molekul')
parser.add_argument('-mult','--mult',type=int,default=1, help='Multiplisitas molekul')
# Input yang berkaitan dengan software, metode, dan jenis pekerjaan
parser.add_argument('-s','--software',type=str,default='orca',help='Software yang digunakan. Pilihan: orca, dcdftb, gromacs')
parser.add_argument('-j','--job',type=str,default='sp',help='Jenis perhitungan yang dilakukan. Pilihan: sp, opt, freq, md, mtd, td, dock.')
parser.add_argument('-m','--method',type=str,default='XTB2',help='Metode yang digunakan dalam perhitungan. Pilihan: XTB, XTB2, DFTB, DFTB2, DFTB3-diag, dan sebagainya.')
# Input yang berkaitan dengan perhitungan frekuensi menggunakan software Orca
parser.add_argument('-sfreq','--scalefreq',type=float,default=1, help='Faktor skala frekuensi yang digunakan.')
# Input yang berkaitan dengan perhitungan menggunakan software DCDFTBMD
parser.add_argument('-disp','--dispersion',type=str,default='None', help='Model koreksi dispersi jika menggunakan software DCDFTB. Pilihan: None, D3, D3BJ, D3H5.')
parser.add_argument('-para','--parapath',type=str,default='/home/adit/opt/dftbplus-21.2/external/slakos/origin/3ob-3-1',help='Lokasi folder berisikan himpunan parameter DFTB yang akan digunakan.')
parser.add_argument('-iter','--iter',type=int,default=500, help='Jumlah iterasi dalam optimasi geometri dan jenis perhitungan lainnya')
parser.add_argument('-ens','--ensembel',type=str,default='NVE', help='Ensembel yang digunakan dalam simulasi dinamika molekul. Pilihan: NVE, NVT, dan NPT.')
parser.add_argument('-tstat','--thermostat',type=str,default='andersen', help='Termostat yang digunakan dalam simulasi NVT. Pilihan: andersen,berendsen,dan nose')
parser.add_argument('-t','--temp', type=float, default=298.15,help='Suhu yang digunakan dalam perhitungan frekuensi maupun simulasi MD dalam satuan Kelvin.')
parser.add_argument('-dt','--deltat',type=float, default=1.0, help='Selang waktu integrasi dalam simulasi dinamika molekul dalam satuan femtodetik.')
parser.add_argument('-mdprint','--mdprint',type=int,default=10, help='Berapa step sekali struktur dicetak. Default=10.')
parser.add_argument('-rest','--restart',type=str,default='false',help='Apakah dilakukan restart simulasi MD?')
parser.add_argument('-nvtdir','--nvtdir',type=str,default='../NVT')
parser.add_argument('-ns','--nstep', type=int, default=50000,help='Banyaknya step dalam simulasi MD.')
parser.add_argument('-np','--nproc',type=int,default=1, help='Jumlah CPU yang digunakan')
# Opsi kondisi PBC
parser.add_argument('-a1','--a1',type=float, default=0, help='panjang vektor a1')
parser.add_argument('-a2','--a2',type=float, default=0, help='panjang vektor a2')
parser.add_argument('-a3','--a3',type=float, default=0, help='panjang vektor a3')
parser.add_argument('-b1','--b1',type=float, default=0, help='panjang vektor b1')
parser.add_argument('-b2','--b2',type=float, default=0, help='panjang vektor b2')
parser.add_argument('-b3','--b3',type=float, default=0, help='panjang vektor b3')
parser.add_argument('-c1','--c1',type=float, default=0, help='panjang vektor c1')
parser.add_argument('-c2','--c2',type=float, default=0, help='panjang vektor c2')
parser.add_argument('-c3','--c3',type=float, default=0, help='panjang vektor c3')
# Input spesifik program DFTB+
parser.add_argument('-hcorr','--hcorr',type=str, default='hdamp',help='Koreksi ikatan hidrogen. Default: hdamp. Pilihan: H5.')
# Input yang berkaitan dengan penyiapan sistem larutan
parser.add_argument('-mt', '--terlarut', type=str, help='Nama file molekul terlarut dalam format .xyz (ditulis tanpa ekstensi).')
parser.add_argument('-ct', '--c_terlarut', type=str, help='Muatan bersih molekul terlarut.',default=0)
parser.add_argument('-pt', '--persen_terlarut', type=str, default=50, help='Persen massa terlarut. Jika lebih dari satu terlarut, pisahkan dengan koma.')
parser.add_argument('-pp', '--persen_pelarut', type=str, default=50, help='Persen massa pelarut. Default:50')
parser.add_argument('-l', '--lapang', type=float, default=5, help='Panjang tambahan (Angstrom) pada rusuk kubus untuk menghindari bad contact. Default: 10.0.')
parser.add_argument('-gen','--generate_dftbinp',type=str,default='false',help='Apakah ingin mengkonversi ke dalam format koordinat xyz?')
parser.add_argument('-mp', '--pelarut', type=str, help='Nama file molekul pelarut dalam format .xyz (ditulis tanpa ekstensi).')
parser.add_argument('-nequil','--nequil',type=int, default=50000, help='Jumlah step pada saat ekuilibrasi.')
parser.add_argument('-nprod','--nprod',type=int, default=400000, help='Jumlah step pada saat production.')
parser.add_argument('-prod', '--production', type=str, default='None', help='Ensembel yang digunakan dalam production run. Pilihan:nve,npt,nvt.')
parser.add_argument('-cp', '--c_pelarut', type=int, default=0, help='Muatan bersih molekul pelarut')
parser.add_argument('-ctype','--charge_type',type=str, default='gas', help='Tipe muatan yang digunakan untuk parameterisasi muatan.')
parser.add_argument('-Nump','--NumPelarut', type=int, default=100, help='Jumlah molekul pelarut maksimum dalam sistem larutan. Default = 100.')
parser.add_argument('-cat','--cation',type=str, default='none',help='Kation yang digunakan untuk menetralkan muatan sistem larutan.')
parser.add_argument('-p', '--pressure', default=1.0, type=float, help='Tekanan dalam satuan bar')
parser.add_argument('--packmol', type=str, default='/home/adit/opt/packmol/packmol')
# Opsi untuk melakukan restart simulasi MD
parser.add_argument('-traj','--traject',type=str, default='../NVT/traject',help='File trayektori dari simulasi sebelumnya')
parser.add_argument('-vel','--velocity',type=str, default='../NVT/velocity',help='File kecepatan atom dari simulasi sebelumnya')
parser.add_argument('-inp','--dftbinp',type=str, default='../NVT/dftb.inp',help='File dftb.inp dari simulasi sebelumnya.')
# Opsi untuk dinding potensial virtual
parser.add_argument('-soft','--soft',type=str,default='false',help='Apakah dinding potensial akan digunakan?. Pilihan: true, false.')
parser.add_argument('-softtype','--softtype',type=str,default='SPHERE',help='Jenis dinding apakah yang akan anda pakai? Baca lebih lanjut manual DCDFTBMD.')
parser.add_argument('-softrange','--softrange',type=float,default=10,help='Ukuran dinding potensial yang anda gunakan. Default = 10 angstrom')
parser.add_argument('-softcenter','--softcenter',type=str,default='COM',help='Jenis pusat koordinat dinding potensial. Default = COM')
parser.add_argument('-metarest','--metarest',type=str,default='false',help='Apakah dilakukan restart simulasi metadinamika?. Pilihan: true, false.')
parser.add_argument('-metafreq','--metafreq',type=int,default=100, help='Dalam berapa step sekali potensial Gaussian ditambahkan?')
parser.add_argument('-metaheight','--metaheight',type=float,default=3.0e-3,help='Ketinggian potensial Gaussian dalam satuan Hartree. Default = 3.0e-3')
parser.add_argument('-cv','--cvtype',type=str,default='coordnum',help='Pilihan collective variable (CV) yang digunakan. Pilihan: coordnum, distance, angle, dihedral, distancediff, distanceadd, meandistance, pointplanedistance.')
parser.add_argument('-metawidth','--metawidth',type=float,default=0.1,help='Lebar potensial Gaussian yang digunakan (dalam satuan yang sama dengan satuan cv). Default = 0.1')
parser.add_argument('-pow1','--pow1',type=float,default=6,help='Nilai pangkat pertama pada definisi bilangan koordinasi rasional. Default = 6')
parser.add_argument('-pow2','--pow2',type=float,default=12,help='Nilai pangkat kedua pada definisi bilangan koordinasi rasional. Default = 12')
parser.add_argument('-rcut','--rcut',type=float,default=1.6,help='Jarak cutoff pada definisi bilangan koordinasi dalam satuan angstrom. Default = 1.6')
parser.add_argument('-fesstart','--fesstart',type=float,default=0, help='Titik minimum CV. Default = 0.')
parser.add_argument('-fesend','--fesend',type=float,default=1, help='Titik maksimum CV. Defalt = 1.')
parser.add_argument('-fesbin','--fesbin',type=float,default=0.01,help='Selang CV. Default = 0.01')
parser.add_argument('-ag1','--ag1',type=str,help='Grup atom pertama dalam sebuah CV.')
parser.add_argument('-ag2','--ag2',type=str,help='Grup atom kedua dalam sebuah CV.')
parser.add_argument('-ag3','--ag3',type=str,help='Grup atom ketiga dalam sebuah CV.')
parser.add_argument('-ag4','--ag4',type=str,help='Grup atom keempat dalam sebuah CV.')
# Input terkait DC setup
parser.add_argument('-bufrad','--bufrad',type=float,default=3.0,help='Radius buffer yang digunakan dalam sebuah subsistem. Default: 3.0')
parser.add_argument('-delta','--delta',type=float,default=3.0,help='Panjang rusuk kubus virual yang dibuat untuk membelah-belah subsistem. Default: 3.0')
parser.add_argument('-opttype','--opttype',type=str,default='bfgs', help='Jenis algoritma optimasi geometri yang digunakan dalam program DFTBUP maupun DCDFTBMD. Default: bfgs. Pilihan: sd, cg, qm, fire.')
parser.add_argument('-freqtype','--freqtype',type=int,default=1, help='Jenis perhitungan frekuensi vibrasi yang dilakukan, analitik (1) atau numerik (2). Default: 1, pilihan: 2.')
parser.add_argument('-econv','--econv',type=float,default=1e-6, help='Batas konvergensi perhitungan energi.')
parser.add_argument('-dconv','--dconv',type=float,default=1e-6, help='Batas konvergensi perhitungan gradien.')
# Input yang berkaitan dengan persiapan docking
parser.add_argument('-ligname','--ligname',type=str,help='Nama ligan yang ingin diekstrak strukturnya')
parser.add_argument('-ligand','--ligand',type=str,help='File ligand dalam format .mol2. Format harus .xyz jika ligand bukan merupakan native ligand.')
parser.add_argument('-dockrange','--dockrange',type=float,default=10,help='Radius yang diperhitungkan sebagai sisi aktif di sekitar ligan asli.')
parser.add_argument('-chargetype','--chargetype',type=str,default='qtpie',help='Tipe muatan parsial untuk ligan. Pilihan: qtpie, gasteiger, eem, eem2015ba, eem2015bm, eem2015bn, eem2015ha, eem2015hm, eem2015hn, eqeq, mmff94, dan qeq.')
parser.add_argument('-calcrmsd','--calcrmsd',type=str,default='no',help='Apakah ingin menghitung RMSD saat docking?')
parser.add_argument('-nlig','--nligands',type=int,help='Jumlah ligan yang akan didocking.')
# Model Pelarut Implisit
parser.add_argument('-solvent','--solvent',type=str,default='none',help='Pelarut yang digunakan dalam perhitungan.')
# Input untuk simulasi MD sistem protein
parser.add_argument('-protein','--protein',type=str,help='Struktur protein dalam format pdb')
# Input untuk perhitungan bergantung waktu
parser.add_argument('-nr','--nroots',type=int,default=5,help='Jumlah orbital aktif yang diperhitungkan dalam perhitungan bergantung waktu.')
parser.add_argument('-tda','--tda',type=str,default='false',help='Apakah akan digunakan pendekatan Tamm-Dancoff. Default = false.')
# Input untuk perhitungan TD-DFTB
parser.add_argument('-ts','--targetstate',type=int,default=0, help='Target orbital transisi yang dituju.')
parser.add_argument('-multtrans','--multtrans',type=int,default=1, help='Multiplisitas spin transisi elektronik.')
parser.add_argument('-ocsstr','--ocsstr',type=str,default='true', help='Menghitung osscilator strength dan momen dipol transisi elektronik.')
parser.add_argument('-wt','--writetrans',type=str,default='true', help='Menulis informasi detail mengenai transisi elektronik yang terjadi.')
parser.add_argument('-lc','--longrange',type=str,default='false', help='Apakah akan dilakukan koreksi interaksi jarak jauh.')
# Input untuk metode multiskala
parser.add_argument('-qmatoms','--qmatoms',type=str,default='None',help='Indeks dari atom-atom di lapisan QM. Indeks dimulai dari nol.')
parser.add_argument('-activeatoms','--activeatoms',type=str,default='1:-1',help='Indeks atom aktif yang digunakan untuk perhitungan.')
parser.add_argument('-hessfile','--hessfile',type=str,default='None',help='File Hessian hasil optimasi geometri atau berbagai perhitungan sebelumnya.')
parser.add_argument('-tc','--totalcharge',type=int,default=0,help='Muatan total molekul.')
parser.add_argument('-tmult','--totalmult',type=int,default=1,help='Multiplisitas spin total molekul.')
parser.add_argument('-qm2method','--qm2method',type=str,default='None',help='Custom method untuk lapisan QM2')
parser.add_argument('-qm2basis','--qm2basis',type=str,default='None',help='Custom himpunan basis untuk lapisan QM2')
# Informasi input padatan
parser.add_argument('-kpts','--kpts',type=str,default='1x1x1',help='Informasi K-points yang digunakan. Ditulis sebagai: 1x1x1, 2x2x2, dsb.')
# Input terkait perhitungan Atom in Molecules
parser.add_argument('-aim','--aim',type=str, default='false',help='Apakah akan dilakukan perhitungan AIM untuk interaksi non-kovalen?')
# Input terkait penggunaan Quantum-Espresso
parser.add_argument('-mode','--mode',type=str,default='from_scratch',help='Mode perhiungan dalam software Quantum-Espresso. Default: from_scratch. Pilihan: from_scratch, restart. ')
parser.add_argument('-pseudo','--pseudo',type=str,default='/home/adit/opt/qe-7.0/pseudo',help='Folder tempat menyimpan file pseudo potential.')
parser.add_argument('-outdir','--outdir',type=str,default='./out',help='Folder tempat menyimpan output.')
parser.add_argument('-unit','--unit',type=str,default='angstrom',help='Satuan yang digunakan dalam mendefinisikan parameter sel dan posisi atom. Default: angstrom. Pilihan: angstrom, bohr')
parser.add_argument('-bravais','--bravais',type=int,default=0,help='Indeks Bravais yang diperlukan untuk mengidentifikasi kristal pada software Quantum-Espresso.')
parser.add_argument('-ecutwfc','--ecutwfc',type=float,default=60.0,help='Cutoff energi kinetik untuk fungsi gelombang dalam satuan Ry. Default: 60.0 Ry.')
parser.add_argument('-ecutrho','--ecutrho',type=float,default=720.0,help='Cutoff energi kinetikr untuk rapat muatan dan potensial. Default: 720.0 Ry.')
parser.add_argument('-mix','--mixing_beta',type=float,default=0.7,help='Koefisien mixing untuk self-consistency.')
parser.add_argument('-conv_thr','--conv_thr',type=float,default=1e-8,help='Batas nilai konvergensi.')
parser.add_argument('-dftfunc','--dftfunc',type=str,default='pbe',help='Fungsional DFT yang digunakan. Default: pbe')
parser.add_argument('-extpseudo','--extpseudo',type=str,default='UPF',help='Ekstensi dari file pseudopotensial. Default: UPF.')
parser.add_argument('-optalgo','--optalgo',type=str,default='bfgs',help='Algoritma untuk optimasi geometri. Default: bfgs. Pilihan: damp, fire, verlet, langevin, langevin-smc, beeman.')
parser.add_argument('-cpress','--cellpress',type=float,default=0.0,help='Tekanan sel dalam satuan kilobar yang digunakan dalam Quantum-Espresso. Default:0.0.')
parser.add_argument('-press_conv','--press_conv_thr',type=float,default=0.5,help='Kriteria konvergensi untuk tekanan sel. Default=0.5 kbar.')
parser.add_argument('-nband','--nband',type=int,default=8,help='Jumlah tingkat energi yang ingin diplot dalam DOS.')
parser.add_argument('-occ','--occ',type=str,default='tetrahedra',help='Metode smearing yang digunakan. Default: tetrahedra. Pilihan: smearing, tetrahedra_lin, tetrahedra_opt, fixed, from_input.')
opt=parser.parse_args(sys.argv[1:])
# Menggunakan molekul dengan format smiles
if ('.xyz' or '.pdb' or 'POSCAR' or '.vasp' or '.poscar') in opt.input:
geom = opt.input
elif '.mol2' in opt.input:
with open('run_babel.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
obabel {} -O geom.xyz""".format(opt.nproc,opt.input),file=fout)
os.system('sbatch run_babel.sh')
geom = 'geom.xyz'
elif ('.mol2' not in opt.input and '.xyz' not in opt.input and '.pdb' not in opt.input and '.vasp' not in opt.input and '.poscar' not in opt.input and 'POSCAR' not in opt.input and '.gen' not in opt.input):
os.system("echo '{}' > geom.smi".format(opt.input))
with open('run_babel.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
obabel geom.smi -O geom.xyz --gen3d""".format(opt.nproc),file=fout)
os.system('sbatch run_babel.sh')
while not os.path.exists('geom.xyz'):
time.sleep(3)
geom = 'geom.xyz'
### ORCA
if opt.software == 'orca':
orca(opt.job,opt.method,opt.nproc,geom,opt.charge,opt.mult,opt.scalefreq,opt.temp,opt.pressure,opt.nroots,opt.tda,opt.solvent,opt.constraints,opt.qmatoms,opt.totalcharge,opt.totalmult,opt.qm2method,opt.qm2basis,opt.activeatoms,opt.hessfile,opt.dispersion,opt.aim)
### NWChem
if opt.software == 'nwchem':
nwchem(opt.job,opt.method,opt.nproc,geom,opt.charge,opt.mult,opt.scalefreq,opt.restart,opt.conv_thr,opt.iter)
### DCDFTBMD
if opt.software == 'dcdftb':
dcdftb(opt.job,opt.method,geom,opt.charge,opt.mult,opt.dispersion,opt.parapath,opt.temp,opt.pressure,opt.ensembel,opt.thermostat,opt.deltat,opt.nstep,opt.mdprint,opt.a1,opt.a2,opt.a3,opt.b1,opt.b2,opt.b3,opt.c1,opt.c2,opt.c3,opt.restart,opt.traject,opt.velocity,opt.dftbinp,opt.soft,opt.softtype,opt.softrange,opt.softcenter,opt.metarest,opt.metafreq,opt.metaheight,opt.cvtype,opt.metawidth,opt.pow1,opt.pow2,opt.rcut,opt.fesstart,opt.fesend,opt.fesbin,opt.ag1,opt.ag2,opt.ag3,opt.ag4,opt.solvent,opt.nroots,opt.targetstate,opt.multtrans,opt.ocsstr,opt.writetrans,opt.longrange,opt.bufrad,opt.delta,opt.opttype,opt.freqtype,opt.econv, opt.dconv)
if opt.software == 'dock':
if opt.job == 'readpdb':
readpdb(opt.input)
if opt.job == 'splitpdb':
splitpdb(opt.input,opt.ligname)
if opt.job == 'addH':
addH(opt.input)
if opt.job == 'addcharge':
addcharge(opt.input,opt.chargetype)
if opt.job == 'sphgen':
sphgen(opt.input)
with open('run_sphgen.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
$DOCK_DIR/sphgen
$DOCK_DIR/sphere_selector protein.sph {} {}""".format(opt.nproc,opt.ligand,opt.dockrange),file=fout)
os.system("sbatch run_sphgen.sh")
if opt.job == 'showsphere':
showsphere()
if opt.job == 'gridgen':
gridgen(opt.input)
with open('run_grid.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
$DOCK_DIR/grid -i grid.in""".format(opt.nproc),file=fout)
os.system("sbatch run_grid.sh")
if opt.job == 'rigiddock':
rigiddock(opt.ligand,opt.calcrmsd)
with open('run_rigiddock.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
$DOCK_DIR/dock6 -i rigid.in -o rigid.out""".format(opt.nproc),file=fout)
os.system("sbatch run_rigiddock.sh")
if opt.job == 'flexdock':
flexdock(opt.ligand,opt.calcrmsd)
with open('run_flexdock.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
$DOCK_DIR/dock6 -i flex.in -o flex.out""".format(opt.nproc),file=fout)
os.system("sbatch run_flexdock.sh")
if opt.job == 'translig':
translig(opt.ligand)
if opt.job=='sdf2xyz' and opt.software == 'dock':
sdf2xyz(opt.ligand)
if opt.job == 'multiflexdock' and opt.software == 'dock':
multiflexdock(opt.nligands,opt.chargetype)
if opt.job == 'multiopt' and opt.software == 'dock':
multiopt(opt.nligands)
if opt.job == 'checkopt' and opt.software == 'dock':
checkopt(opt.nligands)
if opt.software == 'dftb':
if '.xyz' in opt.input:
geom = opt.input
elif 'POSCAR' in opt.input or '.poscar' in opt.input:
poscar2gen(opt.input)
geom = 'in.gen'
elif 'vasp' in opt.input:
vasp2gen(opt.input)
geom = 'in.gen'
dftb(geom,opt.job,opt.activeatoms,opt.method,opt.parapath,opt.dispersion,opt.kpts,opt.hcorr)
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
cp cmmd.in dftb_in.hsd
$DFTB_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout)
os.system('sbatch run.sh')
if opt.software == 'qe':
qe(opt.input,opt.job,opt.mode,opt.pseudo,opt.outdir,opt.bravais,opt.unit,opt.ecutwfc,opt.ecutrho,opt.mixing_beta,opt.conv_thr,opt.dftfunc,opt.extpseudo,opt.kpts,opt.optalgo,opt.cellpress,opt.press_conv_thr,opt.nband,opt.occ)
# RUNNING SCRIPT
if opt.software == 'orca':
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task={}
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe""".format(opt.nproc),file=fout)
os.system('sbatch run.sh')
if opt.software == 'nwchem':
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task={}
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$NWCHEM_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout)
os.system('sbatch run.sh')
if opt.software == 'qe':
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task={}
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
mpirun -np {} $QE_COMMAND < cmmd.in > cmmd.out""".format(opt.nproc,opt.nproc),file=fout)
os.system('sbatch run.sh')
if opt.software == 'dcdftb':
os.system("cp cmmd.in dftb.inp")
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
$DCDFTB_COMMAND
mv dftb.out cmmd.out
mv traject traject.xyz""".format(opt.nproc),file=fout)
os.system('sbatch run.sh')
if opt.software == 'gromacs':
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {}""".format(opt.nproc, opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type),file=fout)
os.system('sbatch run.sh')
if opt.job == 'proprep' and opt.software == 'gmx':
proprep(opt.protein)
if opt.job == 'ligprep' and opt.software == 'gmx':
ligprep(opt.ligand,opt.charge)

@ -0,0 +1,85 @@
#!/usr/bin/env python3
import pymatgen.analysis.adsorption as pa
import pymatgen.core.structure as st
from pymatgen.core import Structure
import argparse
import sys
import warnings
warnings.filterwarnings("ignore")
parser = argparse.ArgumentParser(description='Build possible adsorbate-adsorbent interactions for the surface reaction')
parser.add_argument('-s', '--slab', type=str, help='structure POSCAR of the surface' )
parser.add_argument('-height','--height', type=float, help='height criteria for selection of surface sites' )
parser.add_argument('-d','--distance', type=float, help='distance from the coordinating ensemble of atoms along the miller index for the site (i. e. the distance from the slab itself)' )
parser.add_argument('-pi','--put_inside', default=True, type=bool, help='whether to put the site inside the cell ' )
parser.add_argument('-sr','--symm_reduce', type=float, default=0.1, help='symmetry reduction threshold' )
parser.add_argument('-nr','--near_reduce', type=float, default=0.1, help='near reduction threshold' )
parser.add_argument('-noh','--no_obtuse_hollow', type=bool, default=True, help='flag to indicate whether to include obtuse triangular ensembles in hollow sites' )
parser.add_argument('-sel','--selective_dynamics', type=bool, default=True, help='create the selective dynamics options for VASP calculations')
parser.add_argument('-dyn','--dyn', type=float, default=3.50, help='Height for dynamical atoms selections')
parser.add_argument('-t','--type', type=str, help='Type of adsorption site based on the list' )
parser.add_argument('-ad','--ad', type=str, help='Structure of adsorbate from file' )
parser.add_argument('-all','--all', type=bool, default=False, help='Print all possible structures')
opt = parser.parse_args(sys.argv[1:])
print('Begin searching for adsorption sites...')
# Defining the slab coordinate
slab_coord = Structure.from_file(opt.slab)
# Searching the active sites
check_site = pa.AdsorbateSiteFinder(slab_coord, height=opt.height)
# Preparing the adsorbate molecules in xyz cartesian format
ad = st.Molecule.from_file(opt.ad)
# Defining thke protocol for selective dynamics. Here you need to manually specify the height measured from the top of your slab structure. The default value is 3.50 Angstroms.
adsorbent = pa.AdsorbateSiteFinder(slab_coord, height=opt.dyn, selective_dynamics=opt.selective_dynamics)
adsorbent.slab.to(filename='adsorbent.vasp', fmt='poscar')
# Here, I assume that you want to generate one by one the adsorption types. The choices are 'ontop', 'hollow', and 'bridge' types.
if (opt.all == False):
sites = check_site.find_adsorption_sites(distance=opt.distance, put_inside=opt.put_inside, symm_reduce=opt.symm_reduce, near_reduce=opt.near_reduce, positions=[opt.type], no_obtuse_hollow=opt.no_obtuse_hollow)
site_coord = sites.get(opt.type)
index = 0
site_all = []
for site in site_coord:
adsorbed = adsorbent.add_adsorbate(ad, site, repeat=None, reorient=True)
adsorbed.to(filename='{}_{}.vasp'.format(opt.type,index), fmt='poscar')
index += 1
site_all.append(site.tolist())
# adsorbed = adsorbent.add_adsorbate(ad, site_all, repeat=None, reorient=True)
# adsorbed.to(filename='{}_all.vasp'.format(opt.type), fmt='poscar')
print('{}: {}'.format(opt.type, len(site_coord)))
print('Done for all possibilities of {} adsorption mode!'.format(opt.type))
# The following if in case you want to generate all possible adsorption sites.
else:
sites = check_site.find_adsorption_sites(distance=opt.distance, put_inside=opt.put_inside, symm_reduce=opt.symm_reduce, near_reduce=opt.near_reduce, positions=['hollow','ontop','bridge'], no_obtuse_hollow=opt.no_obtuse_hollow)
hollow_coord = sites.get('hollow')
bridge_coord = sites.get('bridge')
ontop_coord = sites.get('ontop')
hollow_ind = 0
bridge_ind = 0
ontop_ind = 0
for site in hollow_coord:
adsorbed = adsorbent.add_adsorbate(ad, site, repeat=None, reorient=True)
elements = adsorbed.types_of_specie
element = [str(x) for x in elements]
sorted_ads = adsorbed.get_sorted_structure(key=lambda x: element.index(str(x.specie)))
sorted_ads.to(filename='hollow_{}.vasp'.format(hollow_ind), fmt='poscar')
hollow_ind += 1
for site in ontop_coord:
adsorbed = adsorbent.add_adsorbate(ad, site, repeat=None, reorient=True)
elements = adsorbed.types_of_specie
element = [str(x) for x in elements]
sorted_ads = adsorbed.get_sorted_structure(key=lambda x: element.index(str(x.specie)))
sorted_ads.to(filename='ontop_{}.vasp'.format(ontop_ind), fmt='poscar')
ontop_ind += 1
for site in bridge_coord:
adsorbed = adsorbent.add_adsorbate(ad, site, repeat=None, reorient=True)
elements = adsorbed.types_of_specie
element = [str(x) for x in elements]
sorted_ads = adsorbed.get_sorted_structure(key=lambda x: element.index(str(x.specie)))
sorted_ads.to(filename='bridge_{}.vasp'.format(bridge_ind), fmt='poscar')
bridge_ind += 1
print('###############THE LIST OF ADSORPTION SITES####################')
print('hollow:{}, bridge:{}, ontop:{}'.format(len(hollow_coord), len(bridge_coord), len(ontop_coord)))
print('Done for all possibilities of adsorption modes!')

@ -0,0 +1,60 @@
#!/usr/bin/env ruby
require 'matrix'
genfile = ARGV[0]
type = "C"
symbols = []
index = []
coords = []
nat = 0
lat_vector = []
File.open(genfile, "r") do |file|
line = file.gets
arr = line.split
if arr.size > 1
type = arr[1]
end
nat = arr[0].to_i
symbols = file.gets.split
(1..nat).each do |i|
line = file.gets
arr = line.split
index << arr[1].to_i
coords << Vector.elements(arr[2..4].map{|x| x.to_f})
end
if ( type.upcase != "C")
file.gets
(1..3).each do |i|
arr = file.gets.split.map{|x| x.to_f}
lat_vector << Vector.elements(arr)
end
end
end
puts nat
puts
if type.upcase == "C"
(1..nat).each do |i|
puts [symbols[index[i-1]-1], coords[i-1].to_a].to_a.join(" ")
end
elsif type.upcase == "F"
(1..nat).each do |i|
puts [symbols[index[i-1]-1], (coords[i-1][0]*lat_vector[0]+coords[i-1][1]*lat_vector[1]+coords[i-1][2]*lat_vector[2]).to_a.map{|x| "%16.12f"%x}].join(" ")
end
elsif type.upcase == "S"
(1..nat).each do |i|
puts [symbols[index[i-1]-1], coords[i-1].to_a.map{|x| "%16.12f"%x}.join(" ")].to_a.join(" ")
end
end
if ( type.upcase != "C")
puts "TV #{lat_vector[0].to_a.map{|x| "%16.12f"%x}.join(" ")}"
puts "TV #{lat_vector[1].to_a.map{|x| "%16.12f"%x}.join(" ")}"
puts "TV #{lat_vector[2].to_a.map{|x| "%16.12f"%x}.join(" ")}"
end

@ -0,0 +1,81 @@
#!/usr/bin/env ruby
require 'matrix'
lines = []
while line = gets
lines << line
end
title = lines.shift
factor = lines.shift.to_f
basis_vectors = []
3.times do
basis_vectors << lines.shift
end
basis = basis_vectors.map{|x| x.split.map{|y| y.to_f}}
typenames = lines.shift.split
nats = lines.shift.split.map{|x|x.to_i}
selective_dynamics = false
if (lines[0].downcase().start_with?("selective"))
selective_dynamics = true
lines.shift
end
mode_str = lines.shift
mode_type = "S"
if mode_str[0..0].upcase == "D"
mode_name = "Relative"
mode_type = "F"
else
mode_name = "Angstrom"
end
coords = []
nats.each_with_index do |n, i|
n.times do
line = lines.shift.split(" ")
coords << [i+1, line[0..2]]
end
end
final = basis.map{|line| (Vector.elements(line)*factor).to_a}
nat = nats.inject(0){|sum,x| sum + x }
puts "#{nat} #{mode_type}"
puts "#{typenames.join(" ")}"
coords.each_with_index do |line, j|
puts "#{j+1} #{line.join(" ")}"
end
puts "0.0 0.0 0.0"
final.each do |line|
puts line.map{|x| "%20.14f" % x}.join(" ")
end
exit
puts "
TypeNames = { #{typenames.join(" ") } }
TypesAndCoordinates [#{mode}] = {
"
coords.each do |line|
puts " #{line.join(" ")}"
end
puts " }
Periodic = Yes
LatticeVectors [Angstrom] = {
"
puts " }
"

@ -0,0 +1,90 @@
#!/usr/bin/env ruby
require 'ostruct'
input_file = ARGV[0]
def parsexyz(infile)
res = OpenStruct.new
res.coords = []
res.symbols = []
res.natoms = 0
res.title = "POSCAR"
res.tv = []
res.succ = true
res.nats = []
counting_map = {}
counting_map.default = 0
natoms = infile.gets.split[0].to_i
title = infile.gets
natoms.times do
line = infile.gets
arr = line.split
res.symbols << arr[0]
res.coords << arr
counting_map[arr[0]] += 1
end
3.times do
if line = infile.gets and line.include?("TV")
res.tv << line.split(" ")[1..-1]
else
res.tv = [ [20.0, 0.0, 0.0], [0.0, 20.0, 0.0], [0.0, 0.0, 20.0] ]
break
end
end
res.symbols.uniq!
res.symbols.each do |sym|
res.nats << counting_map[sym]
end
return res
end
def writePOSCAR(res)
if (res.title.size == 0)
puts "POSCAR"
else
puts res.title
end
puts 1.0
(0..2).each do |i|
puts res.tv[i].map{|x| "%16.12f" % x}.join(" ")
end
puts res.symbols.join(" ")
puts res.nats.join(" ")
puts "Cart"
res.coords.each do |line|
puts "#{line[1..-1].map{|x| "%16.12f" % x}.join(" ")} #{line[0]}"
end
end
File.open(input_file) do |infile|
num = 0
last_obj = OpenStruct.new
while infile.eof? == false
obj = parsexyz(infile)
num += 1
if obj.succ
last_obj = obj
# last_obj.marshal_load(obj.marshal_dump())
end
end
writePOSCAR(last_obj)
end
exit
File.open(output_file, "w") do |outfile|
outfile.puts [natoms, "C"].join(" ")
outfile.puts symbols.join(" ")
lines.each_with_index do |line, index|
outfile.puts [index+1, symbols.index(line[0])+1, line[1..3]].join(" ")
end
end

File diff suppressed because it is too large Load Diff

@ -0,0 +1,197 @@
#!/usr/bin/env python3
import os
import argparse
import sys
from cmmde_dftb import xyz2gen
import numpy as np
from cmmde_surface import surface
from cmmde_formats import read, write
from cmmde_dftb import xyz2gen
from cmmde_tools import sort
from cmmde_decahedron import Decahedron
from cmmde_icosahedron import Icosahedron
from cmmde_tetrahedron import Tetrahedron
from cmmde_cubic import FaceCenteredCubic, SimpleCubic, BodyCenteredCubic
import pymatgen.analysis.adsorption as pa
import pymatgen.core.structure as st
from pymatgen.core import Structure
import argparse
import sys
import warnings
warnings.filterwarnings("ignore")
parser = argparse.ArgumentParser(description='CMMDEPRE: Program untuk modifikasi input file')
parser.add_argument('-i','--input', type=str, default='',help='Input geometri dalam berbagai format. Format yang didukung: .smi, .mol2, dan semua format yang didukung oleh openbabel.')
parser.add_argument('-j','--job', type=str, default='sp',help='Jenis pekerjaan yang dilakukan.')
parser.add_argument('-s','--size',type=str,help='Ukuran supersel yang ingin dibuat.')
parser.add_argument('-hkl','--hkl',type=str,help='Indeks Miller (hkl) permukaan yang akan dibuat.')
parser.add_argument('-v', '--vacuum', type=float, default=20, help='Tebal lapisan vakum yang dibuat (dalam angstrom). Default: 20 Angstrom.')
parser.add_argument('-n', '--layer', type=int, help='Jumlah lapisan permukaan atau klaster yang akan dibuat.')
parser.add_argument('-ads','--ads',type=str, help='File koordinat Cartesian berisikan molekul adsorbat')
parser.add_argument('-d','--distance',type=float,default=1.5,help='Jarak adsorbat dari lapisan teratas permukaan (Angstrom). Default: 1.5 Angstrom.')
parser.add_argument('-height','--height',type=float,default=2.0, help='Tebal lapisan sisi aktif (Angstrom). Default: 2.0.')
parser.add_argument('-dyn','--dyn',type=float,default=3.0, help='Tebal lapisan bawah permukaan yang dibuat kaku (Angstrom). Default: 3.0.')
parser.add_argument('-e', '--element', type=str, help='Unsur yang akan dibuat klaster' )
parser.add_argument('-t', '--type', type=str, help='Tipe klaster yang akan dibuat. Pilihan: decahedron dan icosahedron')
parser.add_argument('-lc', '--lc', type=float, help='Panjang sel satuan kristal ruah jika dianggap kubus.' )
# Setup untuk klaster decahedron
parser.add_argument('-npar', '--parallel', type=int, help='Jumlah atom pada sisi sejajar dengan ekuatorial.' )
parser.add_argument('-nper', '--perpendicular', type=int, help='Jumlah atom pada sisi tegak lurus dengan ekuatorial.' )
opt = parser.parse_args(sys.argv[1:])
opt = parser.parse_args(sys.argv[1:])
if opt.job == 'smi2xyz':
os.system("echo '{}' > geom.smi".format(opt.input))
with open('run_babel.sh', 'w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel geom.smi -O geom.xyz --gen3d""",file=fout)
os.system('sbatch run_babel.sh')
if opt.job == 'mol2xyz' or opt.job == 'pdb2xyz':
with open('run_babel.sh', 'w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel {} -O geom.xyz""".format(opt.input),file=fout)
os.system('sbatch run_babel.sh')
if opt.job == 'gen2poscar':
from cmmde_gen2poscar import gen2poscar
gen2poscar(opt.input)
if '.mol2' in opt.input and 'charge' in opt.job:
charges = []
with open(opt.input,'r') as f:
lines = f.readlines()
Natom = int(lines[2].split()[0])
for i in range(1,Natom+1):
charges.append(float(lines[7+i].split()[8]))
charges = np.array(charges)
print("Muatan total = {}".format(round(sum(charges))))
if opt.job == 'combinexyz':
xyz = opt.input.split(' ')
natom = 0
coord = []
for i in xyz:
with open(i, 'r') as f:
natom+=int(next(f))
next(f)
for line in f:
coord.append(line.strip())
with open('geom.xyz','w') as f:
print(natom,file=f)
print('Complex file generated by CMMDE',file=f)
for i in coord:
print(i,file=f)
if opt.job == 'supercell':
cell = opt.size.split('x')
filename = opt.input.split('.')[0]
os.system('aflow --supercell={},{},{} < {} > {}_{}{}{}.vasp'.format(cell[0],cell[1],cell[2],opt.input,filename,cell[0],cell[1],cell[2]))
if opt.job == 'surface':
hkl = [int(x) for x in str(opt.hkl)]
bulk = read(opt.input)
slab = surface(bulk, (hkl[0],hkl[1],hkl[2]), opt.layer, vacuum=opt.vacuum)
size = opt.size.split('x')
superslab = slab*(int(size[0]),int(size[1]),1)
superslab_sorted = sort(superslab)
write('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]), superslab_sorted)
# write('slab.vasp', slab*(int(size[0]),int(size[1]),1))
x = []
y = []
z = []
sym = []
a1 = 0
b1 = 0
c1 = 0
a2 = 0
b2 = 0
c2 = 0
a3 = 0
b3 = 0
c3 = 0
with open('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]),'r') as f:
Natoms = int(next(f))
lat = next(f).split('Lattice=')[1].split()
a1+=float(lat[0].strip('"'))
a2+=float(lat[1])
a3+=float(lat[2])
b1+=float(lat[3])
b2+=float(lat[4])
b3+=float(lat[5])
c1+=float(lat[6])
c2+=float(lat[7])
c3+=float(lat[8].strip('"'))
xyz2gen('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]),a1,a2,a3,b1,b2,b3,c1,c2,c3)
from cmmde_gen2poscar import gen2poscar
gen2poscar("in.gen")
os.system("mv in.vasp slab_{}{}{}.vasp".format(hkl[0],hkl[1],hkl[2]))
if opt.job == 'adsorb':
os.system('cmmde_adsorbate.py -s {} -ad {} -all true -dyn {} -height {} -d {}'.format(opt.input,opt.ads,opt.dyn, opt.height, opt.distance))
if opt.job == 'clusadsorb':
os.system('cmmde_xyz2poscar.rb {} > POSCAR'.format(opt.input))
os.system('cmmde_adsorbate.py -s POSCAR -ad {} -all true -dyn {} -height {} -d {}'.format(opt.ads,opt.dyn, opt.height, opt.distance))
if opt.job == 'poscar2xyz':
os.system('cmmde_poscar2gen.rb {} > in.gen'.format(opt.input))
filename = opt.input.split('.')[0]
os.system('cmmde_gen2xyz.rb in.gen > {}.xyz'.format(filename))
if opt.job == 'surfinfo':
moveatoms = []
frozen = []
index = 0
with open(opt.input, 'r') as f:
next(f)
next(f)
next(f)
next(f)
next(f)
next(f)
next(f)
next(f)
next(f)
for line in f:
arr = line.split()
index += 1
if (arr[3] == "T" and arr[4] == "T" and arr[5] == "T"):
moveatoms.append(index)
else:
frozen.append(index)
print('Serial Atom-atom beku:')
for i in frozen:
print(i, end=' ')
print('')
print('Serial Atom-atom aktif:')
for i in moveatoms:
print(i, end=' ')
print('')
if opt.job == 'cluster':
if (opt.type == "icosahedron"):
struct = Icosahedron(opt.element,opt.layer, opt.lc)
struct.write("{}_{}_{}.xyz".format(opt.element,opt.type,opt.layer))
if (opt.type == "decahedron"):
struct = Decahedron(opt.element,opt.perpendicular,opt.parallel,0,opt.lc)
struct.write("{}_{}_{}_{}.xyz".format(opt.element,opt.type,opt.parallel,opt.perpendicular))
if (opt.type == "tetrahedron"):
struct = Tetrahedron(opt.element)

@ -0,0 +1,125 @@
#!/usr/bin/env python3
# pylint: disable=missing-function-docstring
from __future__ import print_function
import panel as pn
from panel_chemistry.widgets import JSMEEditor
from panel.interact import interact
import os
import sys
from panel_chemistry.pane import NGLViewer
from panel_chemistry.pane.ngl_viewer import EXTENSIONS
import py3Dmol
from panel_chemistry.pane import Py3DMol
# from iodata import IOData
def test_can_construct():
JSMEEditor()
def cmmde_gui():
geom = ''
pn.extension("jsme", sizing_mode="stretch_width")
editor = JSMEEditor(value = " ",height=500,format="smiles",subscriptions=['smiles'])
# Terminal widget
terminal = pn.widgets.Terminal(
"Computational Molecular and Material Design Environment\n Authors:\n Universitas Pertamina\n Institut Teknologi Sumatera\n Masyarakat Komputasi Indonesia\n\n",
options = {"cursorBlink": True},
height = 200, sizing_mode = 'stretch_width'
)
# CMMDE software options
software_btn = pn.widgets.MultiSelect(name="Software selections",value=['Orca'],options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'}
# CMMDE job options
job_btn = pn.widgets.MultiChoice(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','Molecular dynamics','Metadynamics'])
job = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq','Molecular dynamics':'md','Metadynamics':'mtd'}
# CMMDE method options
method_btn = pn.widgets.MultiChoice(name="Method selections",value=['GFN2-xTB'],options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag'])
method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'}
# Name your molecule/material
Name_input = pn.widgets.TextInput(name="Molecule name")
# CMMDE running button
Run_btn = pn.widgets.Button(name="Run CMMDE!",button_type='primary')
def run(event):
os.makedirs(Name_input.value)
os.chdir(Name_input.value)
terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(job[job_btn.value[0]]), "-m{}".format(method[method_btn.value[0]]))
Run_btn.on_click(run)
# Post calculations
post_btn = pn.widgets.MultiChoice(name="Post calculation",value=['Frequency calculation'], options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation'])
post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry':'thermo'}
def post_calculation(event):
os.makedirs(post_calc[post_btn.value[0]])
os.chdir(post_calc[post_btn.value[0]])
if post_calc[post_btn.value[0]] == 'thermo' and software[software_btn.value[0]] == 'orca':
terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(software[software_btn.value[0]]))
else:
terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(post_calc[post_btn.value[0]]), "-m{}".format(method[method_btn.value[0]]))
runpost_btn = pn.widgets.Button(name="Run post calculation!",button_type='primary')
runpost_btn.on_click(post_calculation)
# Check the progress
def progress(event):
terminal.subprocess.run("squeue")
Progress_btn = pn.widgets.Button(name="Check calculation",button_type='primary')
Progress_btn.on_click(progress)
# Visualize the results
xyzview = py3Dmol.view()
xyzview.setBackgroundColor('0xeeeeee')
xyzview.zoomTo()
xyzviewer = Py3DMol(xyzview, height=400, sizing_mode="stretch_width",name="CMMDE viewer")
def visualize(event):
with open('cmmd.xyz','r') as f:
xyz = f.read()
xyzview.addModel(xyz,'xyz')
xyzview.setStyle('stick')
xyzviewer.object = xyzview
# xyzviewer.object = xyzview
visual_btn = pn.widgets.Button(name="Visualize!", button_type='primary')
visual_btn.on_click(visualize)
def set_background(color='0xeeeeee'):
xyzview.setBackgroundColor(color)
xyzviewer.param.trigger("object")
set_background("#e6f6ff")
accent = "#0072B5"
# background = pn.widgets.ColorPicker(value="#e6f6ff", name="Background")
# pn.bind(set_background, color=background, watch=True)
# def set_style(style="stick"):
# xyzview.setStyle({style: {}})
# xyzview.zoomTo()
# xyzviewer.param.trigger("object")
# set_style("stick")
# style=pn.widgets.RadioButtonGroup(value="stick", options=["stick", "sphere"], name="Style", button_type="success")
# set_style=pn.bind(set_style, style=style, watch=True)
#### Wrap them all together ##########
return pn.template.FastListTemplate(
site="CMMDE-GUI",
title="CMMDE Editor",
main=[editor, terminal, terminal.subprocess.param.running,visual_btn,pn.Tabs(xyzviewer)],
sidebar=[pn.Row(software_btn,height=200),Name_input,pn.Column(job_btn, height=400),pn.Column(method_btn,height=400),pn.Row(Run_btn,Progress_btn),pn.Column(post_btn,height=400),pn.Row(runpost_btn,Progress_btn)],
header_background=accent, accent_base_color=accent
)
if __name__.startswith("bokeh"):
cmmde_gui().servable()

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@ -0,0 +1,34 @@
#
# Number of atoms
#
5
#
# The current total energy in Eh
#
-4.174453278190
#
# The current gradient in Eh/bohr
#
-0.000009007707
-0.000001022543
-0.000028029012
0.011370019952
0.000004146566
0.000007643366
-0.003786329235
0.003636059856
-0.010072248687
-0.003784129718
0.006913091591
0.008198977151
-0.003790553292
-0.010552275470
0.001893657182
#
# The atomic numbers and current coordinates in Bohr
#
6 1.8082282 -0.1155039 -0.1255024
1 3.8862633 -0.1154577 -0.1253829
1 1.1155667 0.5496500 -1.9682689
1 1.1156455 1.1478457 1.3720151
1 1.1155587 -2.0439966 0.2199578

Binary file not shown.

@ -0,0 +1,192 @@
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-4.174453
$hessian
15
0 1 2 3 4
0 4.7636737984E-01 9.8065926338E-06 4.0509474611E-05 -2.6387163902E-01 -4.9481781065E-06
1 9.8065926338E-06 4.7636874797E-01 -3.5322753161E-05 -4.4553523828E-06 -4.6712723347E-02
2 4.0509474611E-05 -3.5322753161E-05 4.7642267416E-01 -1.2244706595E-05 1.3445702371E-06
3 -2.6387163902E-01 -4.4553523828E-06 -1.2244706595E-05 3.0569963803E-01 3.1934909046E-06
4 -4.9481781065E-06 -4.6712723347E-02 1.3445702371E-06 3.1934909046E-06 4.9654687555E-02
5 -1.3149822728E-05 1.3436762125E-06 -4.6713637453E-02 1.0441682149E-05 5.2350354108E-07
6 -7.0839334605E-02 2.3174998109E-02 -6.4209878747E-02 -1.3938723600E-02 1.0841749785E-02
7 2.3175171407E-02 -6.8961088744E-02 6.1660244645E-02 6.2463766555E-04 -1.9733379734E-04
8 -6.4209650586E-02 6.1659527473E-02 -2.1753160526E-01 -1.7300159651E-03 6.4963338353E-04
9 -7.0831022262E-02 4.3995634311E-02 5.2150044298E-02 -1.3942892159E-02 2.0594374742E-02
10 4.3995912265E-02 -1.2696536462E-01 -9.5129410929E-02 1.1882102059E-03 -8.0894314407E-04
11 5.2150455969E-02 -9.5129546775E-02 -1.5947516242E-01 1.4084470151E-03 -1.0045758742E-03
12 -7.0837646203E-02 -6.7175983361E-02 1.2031570067E-02 -1.3939157729E-02 -3.1434370036E-02
13 -6.7175915060E-02 -2.3374165050E-01 3.3503139526E-02 -1.8110895566E-03 -1.9348846781E-03
14 1.2031855740E-02 3.3503990448E-02 -5.2714172578E-02 3.2464202323E-04 3.5307530516E-04
5 6 7 8 9
0 -1.3149822728E-05 -7.0839334605E-02 2.3175171407E-02 -6.4209650586E-02 -7.0831022262E-02
1 1.3436762125E-06 2.3174998109E-02 -6.8961088744E-02 6.1659527473E-02 4.3995634311E-02
2 -4.6713637453E-02 -6.4209878747E-02 6.1660244645E-02 -2.1753160526E-01 5.2150044298E-02
3 1.0441682149E-05 -1.3938723600E-02 6.2463766555E-04 -1.7300159651E-03 -1.3942892159E-02
4 5.2350354108E-07 1.0841749785E-02 -1.9733379734E-04 6.4963338353E-04 2.0594374742E-02
5 4.9655550291E-02 -3.0037506737E-02 6.5000245392E-04 -1.7635556184E-03 2.4410415586E-02
6 -3.0037506737E-02 7.8101558840E-02 -2.7323500177E-02 7.5703379066E-02 3.3391028845E-03
7 6.5000245392E-04 -2.7323500177E-02 7.5886724901E-02 -7.2696444954E-02 -6.1280276453E-03
8 -1.7635556184E-03 7.5703379066E-02 -7.2696444954E-02 2.5105105304E-01 -7.7284477870E-03
9 2.4410415586E-02 3.3391028845E-03 -6.1280276453E-03 -7.7284477870E-03 7.8097057948E-02
10 -1.0046717260E-03 -3.0650673504E-03 5.6305999555E-03 6.6430798619E-03 -5.1877079575E-02
11 -1.1518223626E-03 9.3745302500E-03 -1.7929175053E-02 -2.4869250248E-02 -6.1492402669E-02
12 5.6297988854E-03 3.3390756247E-03 9.6509362855E-03 -2.0330968182E-03 3.3394321869E-03
13 3.5280279411E-04 -3.6290316847E-03 -1.2357232660E-02 3.7418875799E-03 -6.5863631195E-03
14 -2.5744191699E-05 9.1708936904E-03 2.8314023659E-02 -6.8818696287E-03 -7.3415421228E-03
10 11 12 13 14
0 4.3995912265E-02 5.2150455969E-02 -7.0837646203E-02 -6.7175915060E-02 1.2031855740E-02
1 -1.2696536462E-01 -9.5129546775E-02 -6.7175983361E-02 -2.3374165050E-01 3.3503990448E-02
2 -9.5129410929E-02 -1.5947516242E-01 1.2031570067E-02 3.3503139526E-02 -5.2714172578E-02
3 1.1882102059E-03 1.4084470151E-03 -1.3939157729E-02 -1.8110895566E-03 3.2464202323E-04
4 -8.0894314407E-04 -1.0045758742E-03 -3.1434370036E-02 -1.9348846781E-03 3.5307530516E-04
5 -1.0046717260E-03 -1.1518223626E-03 5.6297988854E-03 3.5280279411E-04 -2.5744191699E-05
6 -3.0650673504E-03 9.3745302500E-03 3.3390756247E-03 -3.6290316847E-03 9.1708936904E-03
7 5.6305999555E-03 -1.7929175053E-02 9.6509362855E-03 -1.2357232660E-02 2.8314023659E-02
8 6.6430798619E-03 -2.4869250248E-02 -2.0330968182E-03 3.7418875799E-03 -6.8818696287E-03
9 -5.1877079575E-02 -6.1492402669E-02 3.3394321869E-03 -6.5863631195E-03 -7.3415421228E-03
10 1.4428067706E-01 1.1216627263E-01 9.7565379841E-03 -2.2133354919E-02 -2.2671723378E-02
11 1.1216627263E-01 1.8260820267E-01 -1.4427922682E-03 1.9002273053E-03 2.8931816346E-03
12 9.7565379841E-03 -1.4427922682E-03 7.8099975098E-02 7.9204668253E-02 -1.4186255518E-02
13 -2.2133354919E-02 1.9002273053E-03 7.9204668253E-02 2.7017311542E-01 -3.9500247375E-02
14 -2.2671723378E-02 2.8931816346E-03 -1.4186255518E-02 -3.9500247375E-02 5.6729796094E-02
$vibrational_frequencies
15
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1411.894158
7 1411.942387
8 1411.989208
9 1567.724975
10 1567.756664
11 2918.147432
12 2930.722274
13 2930.813685
14 2930.996046
$normal_modes
15 15
0 1 2 3 4
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
6 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
10 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
11 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
12 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
13 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
14 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 6 7 8 9
0 0.0000000000E+00 9.6477903682E-02 6.9838285112E-02 5.0247657476E-02 1.0285495508E-05
1 0.0000000000E+00 -6.5244195857E-02 1.0860033168E-01 -2.5674116800E-02 -1.0798405126E-05
2 0.0000000000E+00 -5.6088574999E-02 -6.1989041273E-03 1.1629676616E-01 -7.5696185494E-06
3 0.0000000000E+00 4.2224433199E-02 3.0585059656E-02 2.2027491770E-02 1.1770838068E-05
4 0.0000000000E+00 3.0574268985E-01 -5.0895242725E-01 1.2037823767E-01 4.2177266162E-01
5 0.0000000000E+00 2.6292699701E-01 2.9150057128E-02 -5.4508701960E-01 -2.6859136081E-01
6 0.0000000000E+00 -4.4663913988E-01 -3.5644404675E-01 -1.6705301932E-02 3.7314153890E-01
7 0.0000000000E+00 3.0044265391E-01 -4.8132377619E-01 -8.9851299978E-02 -2.4247029500E-01
8 0.0000000000E+00 2.7795616746E-01 -4.8141902391E-02 3.7122287366E-02 -2.2777215718E-01
9 0.0000000000E+00 -2.6047059427E-01 -3.9261870970E-01 -3.2337347124E-01 6.2793968834E-02
10 0.0000000000E+00 -4.3850669339E-02 -3.8972868840E-01 2.8067701807E-01 -3.6444449307E-01
11 0.0000000000E+00 -1.5166137869E-01 1.7045603953E-01 -3.5509072322E-01 3.3649266944E-01
12 0.0000000000E+00 -4.8471400571E-01 -1.1369258345E-01 -2.8068345465E-01 -4.3606983719E-01
13 0.0000000000E+00 2.1509393316E-01 8.5958677760E-02 -5.2795342450E-03 1.8527079673E-01
14 0.0000000000E+00 2.7911142286E-01 -7.7600069791E-02 -5.2269896754E-01 1.5996104566E-01
10 11 12 13 14
0 1.9204652077E-05 -5.4805850258E-05 -4.1798508139E-02 -6.7803732330E-02 3.4456264823E-02
1 2.0564924792E-05 6.8646694199E-05 6.0729309089E-02 -5.3425545265E-02 -3.1456376564E-02
2 9.6100321186E-06 -6.9645773690E-04 4.5782854569E-02 8.9593147936E-03 7.3181607166E-02
3 2.5534976406E-05 5.0051084360E-01 4.1636224744E-01 6.7286481475E-01 -3.3775125382E-01
4 -2.6872468668E-01 3.7454611147E-05 2.9774155047E-02 -2.6169302021E-02 -1.5414189686E-02
5 -4.2176170002E-01 -3.2676870747E-04 2.2463737380E-02 4.4214525483E-03 3.5838244132E-02
6 2.8791652277E-01 -1.6441255022E-01 -4.6171136093E-02 -4.1860475240E-02 -2.8431296913E-01
7 4.0677554581E-01 1.5789223761E-01 5.4429591353E-02 -1.7893642594E-02 2.7381977344E-01
8 3.8608146478E-02 -4.3768539857E-01 -4.5893125785E-02 -1.8572459712E-02 -7.6545794522E-01
9 -4.6732937548E-01 -1.6820033754E-01 2.6974086174E-01 -4.5257667378E-02 9.2311851128E-02
10 -1.5748775713E-01 3.0678667384E-01 -4.9963292343E-01 -4.2590214260E-03 -1.5299492287E-01
11 -8.3277284963E-02 3.6326100083E-01 -6.0508221964E-01 3.0380954142E-02 -1.2722379425E-01
12 1.7915848135E-01 -1.6724490716E-01 -1.4187455121E-01 2.2218053919E-01 1.1918273215E-01
13 1.9191853047E-02 -4.6553433773E-01 -3.0820150894E-01 6.8492337892E-01 2.6941328644E-01
14 4.6631632849E-01 8.3049930218E-02 8.2978010602E-02 -1.2298622673E-01 -1.5164722587E-02
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
5
C 12.01100 1.808228232708 -0.115503926643 -0.125502358011
H 1.00800 3.886263342700 -0.115457665877 -0.125382884353
H 1.00800 1.115566681275 0.549649980043 -1.968268883378
H 1.00800 1.115645469129 1.147845717277 1.372015106814
H 1.00800 1.115558681105 -2.043996616803 0.219957812341
$actual_temperature
0.000000
$frequency_scale_factor
1.000000
$dipole_derivatives
15
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
-2.0000000000E-01 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
-0.0000000000E+00 0.0000000000E+00 -2.0000000000E-01
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01
0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00
0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00
-0.0000000000E+00 -2.0000000000E-01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
#
# The IR spectrum
# wavenumber eps Int TX TY TZ
#
$ir_spectrum
15
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
1411.89 0.00073546 3.71673613 -0.001597 -0.008137 -0.009685
1411.94 0.00043621 2.20441932 -0.001157 -0.003252 0.009192
1411.99 0.00020721 1.04716171 -0.000833 0.000200 -0.006713
1567.72 0.00154955 7.83078993 -0.000000 -0.007232 0.016004
1567.76 0.00001515 0.07656697 -0.000001 -0.000749 0.001567
2918.15 0.00419539 21.20180047 -0.014320 0.013320 0.008134
2930.72 0.00251671 12.71842438 -0.011427 0.008458 0.008116
2930.81 0.00652390 32.96909208 -0.018466 -0.018797 0.000568
2931.00 0.00633467 32.01283832 0.009269 -0.007394 0.023106
$end

@ -0,0 +1,13 @@
#CMMDE generated Orca input file
!XTB2 Numfreq
%pal
nprocs 1
end
*xyzfile 0 1 cmmd.xyz
%freq
scalfreq 1
Temp 298.15
Pressure 1.0
end

@ -0,0 +1,164 @@
$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
2 15
1.80826004 -0.11550006 -0.12544002 3.87220003 -0.11550006 -0.12544002
1.12026745 0.54514820 -1.95577206 1.12026745 1.13931589 1.36186893
1.12026745 -2.03092647 0.21760196
1.80823704 -0.11549999 -0.12548122 3.88617549 -0.11547122 -0.12540627
1.11560506 0.54961930 -1.96816875 1.11565113 1.14779680 1.37193952
1.11559369 -2.04390740 0.21993552
# redundant internal coordinates
# nbonds nangles ndihedrals nimpropers ncartesians
# bond definitions A B
# angle definitions A B C
# dihedral definitions A B C D
# improper torsion definitions A B C D
# cartesian definitions A x/y/z
$redundant_internals
4 6 0 0 0
1 0 0
2 0 0
3 0 0
4 0 0
1 0 3 0 0
2 0 3 0 0
1 0 4 0 0
2 0 4 0 0
3 0 4 0 0
1 0 2 0 0
$energies
2
-40.4517849381878705
-40.4519245409608246
$gradients
2 15
0.0000281120249107 -0.0000037064411669 0.0000525165778874 -0.0049990129430250
-0.0000045316433501 0.0000098634302251 0.0016701552391622 -0.0015882790949084
0.0044334055573350 0.0016586340354712 -0.0030330170283499 -0.0035893738581539
0.0016688694657209 0.0046447102314975 -0.0008246575087751
0.0000109936929351 0.0000063540709450 0.0000318229732579 -0.0000294208486349
-0.0000021914169169 0.0000138398073834 0.0000203548871545 -0.0000037180473361
0.0000440886074016 0.0000094316758080 -0.0000186102122881 -0.0000130949132512
0.0000130715741403 0.0000344084933163 0.0000033464078443
$redundant_coords
2 10
2.0639399862074517 2.0639538051479716 2.0639730605185891 2.0639452371510258
1.9106340448094910 1.9106237183363008 1.9106388109628560 1.9106351045974839
1.9106303954694328 1.9106373432471970
2.0779384518561348 2.0778883651837607 2.0779467901700923 2.0779371257260508
1.9105645779003646 1.9106531722343145 1.9106392975229700 1.9106648467042662
1.9106137724204406 1.9106637475244237
$redundant_gradients
2 10
-0.0050043645066456 -0.0049813849297886 -0.0049952006081833 -0.0050019622241142
0.0000201718064817 -0.0000085529895258 -0.0000001414303179 -0.0000086367530628
0.0000048268874594 -0.0000076675152472
-0.0000343072826948 -0.0000322949407078 -0.0000357710991749 -0.0000337494803822
0.0000116868532667 -0.0000047060577191 -0.0000004911749077 -0.0000044784875371
0.0000028621663169 -0.0000048722788676
$hessian_approx
15 15
0 1 2 3 4 5
0 0.839489 0.000005 0.000001 -0.357113 0.000000 0.000001
1 0.000005 0.839479 -0.000008 0.000060 -0.136205 0.000001
2 0.000001 -0.000008 0.839466 0.000280 0.000001 -0.136202
3 -0.357113 0.000060 0.000280 0.356650 -0.000050 -0.000126
4 0.000000 -0.136205 0.000001 -0.000050 0.102153 -0.000001
5 0.000001 0.000001 -0.136202 -0.000126 -0.000001 0.102152
6 -0.160793 0.023559 -0.065423 0.000164 0.021816 -0.060351
7 0.023611 -0.158825 0.062823 -0.000161 0.002601 -0.007289
8 -0.065420 0.062681 -0.310252 0.000457 -0.007205 0.020195
9 -0.160787 0.044765 0.052991 0.000084 0.041419 0.049116
10 0.044847 -0.217845 -0.096648 -0.000331 0.009409 0.011112
11 0.053157 -0.096774 -0.250752 -0.000490 0.011152 0.013170
12 -0.160796 -0.068388 0.012151 0.000173 -0.063185 0.011361
13 -0.068464 -0.326605 0.033831 0.000502 0.022042 -0.003822
14 0.012261 0.034100 -0.142260 -0.000152 -0.003947 0.000685
6 7 8 9 10 11
0 -0.160793 0.023611 -0.065420 -0.160787 0.044847 0.053157
1 0.023559 -0.158825 0.062681 0.044765 -0.217845 -0.096774
2 -0.065423 0.062823 -0.310252 0.052991 -0.096648 -0.250752
3 0.000164 -0.000161 0.000457 0.000084 -0.000331 -0.000490
4 0.021816 0.002601 -0.007205 0.041419 0.009409 0.011152
5 -0.060351 -0.007289 0.020195 0.049116 0.011112 0.013170
6 0.130445 -0.027167 0.075264 0.015113 -0.017703 0.022163
7 -0.027167 0.128238 -0.072271 -0.024314 0.028526 -0.035545
8 0.075264 -0.072271 0.302367 -0.014531 0.017288 -0.020652
9 0.015113 -0.024314 -0.014531 0.130495 -0.051638 -0.061174
10 -0.017703 0.028526 0.017288 -0.051638 0.196223 0.111445
11 0.022163 -0.035545 -0.020652 -0.061174 0.111445 0.234173
12 0.015084 0.028017 0.004267 0.015111 0.024801 -0.013686
13 -0.000511 -0.000534 -0.000510 -0.010238 -0.016301 0.009736
14 0.028356 0.052273 0.008369 -0.026390 -0.043216 0.024039
12 13 14
0 -0.160796 -0.068464 0.012261
1 -0.068388 -0.326605 0.034100
2 0.012151 0.033831 -0.142260
3 0.000173 0.000502 -0.000152
4 -0.063185 0.022042 -0.003947
5 0.011361 -0.003822 0.000685
6 0.015084 -0.000511 0.028356
7 0.028017 -0.000534 0.052273
8 0.004267 -0.000510 0.008369
9 0.015111 -0.010238 -0.026390
10 0.024801 -0.016301 -0.043216
11 -0.013686 0.009736 0.024039
12 0.130441 0.078750 -0.014083
13 0.078750 0.321380 -0.039205
14 -0.014083 -0.039205 0.109162
$bmatrix
10 15
0 1 2 3 4 5
0 -1.000000 -0.000014 -0.000036 1.000000 0.000014 0.000036
1 0.333335 -0.320094 0.886808 0.000000 0.000000 0.000000
2 0.333303 -0.607954 -0.720625 0.000000 0.000000 0.000000
3 0.333332 0.928039 -0.166231 0.000000 0.000000 0.000000
4 0.453709 0.413743 0.490435 0.000018 -0.310318 -0.367832
5 -0.453718 0.631637 -0.113097 0.000000 0.000000 0.000000
6 0.453727 -0.631604 0.113159 -0.000003 0.473706 -0.084857
7 -0.453744 -0.413783 -0.490432 0.000000 0.000000 0.000000
8 -0.453692 -0.217839 0.603568 0.000000 0.000000 0.000000
9 0.453748 0.217869 -0.603547 -0.000014 -0.163392 0.452660
6 7 8 9 10 11
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 -0.333335 0.320094 -0.886808 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 -0.333303 0.607954 0.720625
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 -0.453727 -0.103425 -0.122603
5 0.226857 -0.364801 -0.216946 0.226861 -0.266836 0.330043
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.226874 0.419254 0.066052 0.000000 0.000000 0.000000
8 0.000000 0.000000 0.000000 0.226850 0.370268 -0.207453
9 -0.453734 -0.054476 0.150887 0.000000 0.000000 0.000000
12 13 14
0 0.000000 0.000000 0.000000
1 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000
3 -0.333332 -0.928039 0.166231
4 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000
6 -0.453724 0.157898 -0.028302
7 0.226870 -0.005472 0.424380
8 0.226841 -0.152429 -0.396114
9 0.000000 0.000000 0.000000

@ -0,0 +1,715 @@
*****************
* O R C A *
*****************
#,
###
####
#####
######
########,
,,################,,,,,
,,#################################,,
,,##########################################,,
,#########################################, ''#####,
,#############################################,, '####,
,##################################################,,,,####,
,###########'''' ''''###############################
,#####'' ,,,,##########,,,, '''####''' '####
,##' ,,,,###########################,,, '##
' ,,###'''' '''############,,,
,,##'' '''############,,,, ,,,,,,###''
,#'' '''#######################'''
' ''''####''''
,#######, #######, ,#######, ##
,#' '#, ## ## ,#' '#, #''# ###### ,####,
## ## ## ,#' ## #' '# # #' '#
## ## ####### ## ,######, #####, # #
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,#
'#######' ## ## '#######' #' '# #####' # '####'
#######################################################
# -***- #
# Department of theory and spectroscopy #
# Directorship and core code : Frank Neese #
# Max Planck Institute fuer Kohlenforschung #
# Kaiser Wilhelm Platz 1 #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 5.0.2 - RELEASE -
With contributions from (in alphabetic order):
Daniel Aravena : Magnetic Suceptibility
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation)
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum
Ute Becker : Parallelization
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD
Martin Brehm : Molecular dynamics
Dmytro Bykov : SCF Hessian
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE
Dipayan Datta : RHF DLPNO-CCSD density
Achintya Kumar Dutta : EOM-CC, STEOM-CC
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
Lee Huntington : MR-EOM, pCC
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
Marcus Kettner : VPT2
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
Martin Krupicka : Initial AUTO-CI
Lucas Lang : DCDCAS
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC
Dagmar Lenk : GEPOL surface, SMD
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization
Dimitrios Manganas : Further ROCIS development; embedding schemes
Dimitrios Pantazis : SARC Basis sets
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient
Christoph Reimann : Effective Core Potentials
Marius Retegan : Local ZFS, SOC
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB
Michael Roemelt : Original ROCIS implementation
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density
Barbara Sandhoefer : DKH picture change effects
Avijit Sen : IP-ROCIS
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
Bernardo de Souza : ESD, SOC TD-DFT
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
Willem Van den Heuvel : Paramagnetic NMR
Boris Wezisla : Elementary symmetry handling
Frank Wennmohs : Technical directorship
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization,
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Jiri Pittner, Ondrej Demel : Mk-CCSD
Frank Weinhold : gennbo (NPA and NBO analysis)
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
Lars Goerigk : TD-DFT with DH, B97 family of functionals
V. Asgeirsson, H. Jonsson : NEB implementation
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
nearIR, NL-DFT gradient (VV10), updates on ESD,
ML-optimized integration grids
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library
Liviu Ungur et al : ANISO software
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
Your ORCA version has been built with support for libXC version: 5.1.0
For citations please refer to: https://tddft.org/programs/libxc/
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
SCALAPACK package : Parallel linear algebra routines
Shared memory : Shared parallel matrices
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
Core in use : SkylakeX
Copyright (c) 2011-2014, The OpenBLAS Project
***************************************
The coordinates will be read from file: cmmd.xyz
***************************************
Your calculation utilizes the semiempirical GFN2-xTB method
Please cite in your paper:
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652.
================================================================================
================================================================================
WARNINGS
Please study these warnings very carefully!
================================================================================
WARNING: Old DensityContainer found on disk!
Will remove this file -
If you want to keep old densities, please start your calculation with a different basename.
WARNING: Gradients needed for Numerical Frequencies
===> : Setting RunTyp to EnGrad
WARNING: Found dipole moment calculation with XTB calculation
===> : Switching off dipole moment calculation
WARNING: TRAH-SCF for XTB is not implemented!
===> : Turning TRAH off!
================================================================================
INPUT FILE
================================================================================
NAME = cmmd.in
| 1> #CMMDE generated Orca input file
| 2> !XTB2 Numfreq
| 3> %pal
| 4> nprocs 1
| 5> end
| 6>
| 7> *xyzfile 0 1 cmmd.xyz
| 8>
| 9> %freq
| 10> scalfreq 1
| 11> Temp 298.15
| 12> Pressure 1.0
| 13> end
| 14>
| 15> ****END OF INPUT****
================================================================================
*******************************
* Energy+Gradient Calculation *
*******************************
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/04/28 at 11:27:15.724
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 5
number of electrons : 8
charge : 0
spin : 0.0
first test random number : 0.45806096902679
ID Z sym. atoms
1 6 C 1
2 1 H 2-5
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
...................................................
: SETUP :
:.................................................:
: # basis functions 8 :
: # atomic orbitals 8 :
: # shells 6 :
: # electrons 8 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -4.2239587 -0.422396E+01 0.248E+00 16.90 0.0 T
2 -4.2374347 -0.134760E-01 0.912E-01 16.71 1.0 T
3 -4.2375727 -0.137987E-03 0.506E-01 16.61 1.0 T
4 -4.2376226 -0.499077E-04 0.100E-01 16.49 1.0 T
5 -4.2376226 0.183268E-07 0.539E-03 16.49 8.3 T
6 -4.2376227 -0.794093E-07 0.166E-04 16.49 269.4 T
7 -4.2376227 -0.834559E-10 0.196E-06 16.49 22792.6 T
*** convergence criteria satisfied after 7 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.5788386 -15.7510
2 2.0000 -0.4661696 -12.6851
3 2.0000 -0.4661655 -12.6850
4 2.0000 -0.4661594 -12.6848 (HOMO)
5 0.1398593 3.8058 (LUMO)
6 0.2020304 5.4975
7 0.2020678 5.4985
8 0.2021139 5.4998
-------------------------------------------------------------
HL-Gap 0.6060187 Eh 16.4906 eV
Fermi-level -0.1631500 Eh -4.4395 eV
SCC (total) 0 d, 0 h, 0 min, 0.023 sec
SCC setup ... 0 min, 0.000 sec ( 1.260%)
Dispersion ... 0 min, 0.000 sec ( 0.106%)
classical contributions ... 0 min, 0.000 sec ( 0.058%)
integral evaluation ... 0 min, 0.001 sec ( 2.896%)
iterations ... 0 min, 0.021 sec ( 94.189%)
molecular gradient ... 0 min, 0.000 sec ( 0.973%)
printout ... 0 min, 0.000 sec ( 0.466%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -4.174453278189 Eh ::
:: gradient norm 0.022735966218 Eh/a0 ::
:: HOMO-LUMO gap 16.490609280094 eV ::
::.................................................::
:: SCC energy -4.237622656391 Eh ::
:: -> isotropic ES 0.001892323517 Eh ::
:: -> anisotropic ES 0.002670073781 Eh ::
:: -> anisotropic XC 0.004009252448 Eh ::
:: -> dispersion -0.000663926968 Eh ::
:: repulsion energy 0.063169371945 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -4.174453278189 Eh |
| GRADIENT NORM 0.022735966218 Eh/α |
| HOMO-LUMO GAP 16.490609280094 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/04/28 at 11:27:15.762
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.038 sec
* cpu-time: 0 d, 0 h, 0 min, 0.009 sec
* ratio c/w: 0.247 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.023 sec
* cpu-time: 0 d, 0 h, 0 min, 0.002 sec
* ratio c/w: 0.094 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -4.174453278190
------------------------- --------------------
----------------------------------------------------------------------------
ORCA NUMERICAL FREQUENCIES
----------------------------------------------------------------------------
Number of atoms ... 5
Central differences ... used
Number of displacements ... 30
Numerical increment ... 5.000e-03 bohr
IR-spectrum generation ... on
Raman-spectrum generation ... off
Surface Crossing Hessian ... off
The output will be reduced. Please look at the following files:
SCF program output ... >cmmd.lastscf
Integral program output ... >cmmd.lastint
Gradient program output ... >cmmd.lastgrad
Dipole moment program output ... >cmmd.lastmom
AutoCI program output ... >cmmd.lastautoci
<< Calculating on displaced geometry 1 (of 30) >>
<< Calculating on displaced geometry 2 (of 30) >>
<< Calculating on displaced geometry 3 (of 30) >>
<< Calculating on displaced geometry 4 (of 30) >>
<< Calculating on displaced geometry 5 (of 30) >>
<< Calculating on displaced geometry 6 (of 30) >>
<< Calculating on displaced geometry 7 (of 30) >>
<< Calculating on displaced geometry 8 (of 30) >>
<< Calculating on displaced geometry 9 (of 30) >>
<< Calculating on displaced geometry 10 (of 30) >>
<< Calculating on displaced geometry 11 (of 30) >>
<< Calculating on displaced geometry 12 (of 30) >>
<< Calculating on displaced geometry 13 (of 30) >>
<< Calculating on displaced geometry 14 (of 30) >>
<< Calculating on displaced geometry 15 (of 30) >>
<< Calculating on displaced geometry 16 (of 30) >>
<< Calculating on displaced geometry 17 (of 30) >>
<< Calculating on displaced geometry 18 (of 30) >>
<< Calculating on displaced geometry 19 (of 30) >>
<< Calculating on displaced geometry 20 (of 30) >>
<< Calculating on displaced geometry 21 (of 30) >>
<< Calculating on displaced geometry 22 (of 30) >>
<< Calculating on displaced geometry 23 (of 30) >>
<< Calculating on displaced geometry 24 (of 30) >>
<< Calculating on displaced geometry 25 (of 30) >>
<< Calculating on displaced geometry 26 (of 30) >>
<< Calculating on displaced geometry 27 (of 30) >>
<< Calculating on displaced geometry 28 (of 30) >>
<< Calculating on displaced geometry 29 (of 30) >>
<< Calculating on displaced geometry 30 (of 30) >>
-----------------------
VIBRATIONAL FREQUENCIES
-----------------------
Scaling factor for frequencies = 1.000000000 (already applied!)
0: 0.00 cm**-1
1: 0.00 cm**-1
2: 0.00 cm**-1
3: 0.00 cm**-1
4: 0.00 cm**-1
5: 0.00 cm**-1
6: 1411.89 cm**-1
7: 1411.94 cm**-1
8: 1411.99 cm**-1
9: 1567.72 cm**-1
10: 1567.76 cm**-1
11: 2918.15 cm**-1
12: 2930.72 cm**-1
13: 2930.81 cm**-1
14: 2931.00 cm**-1
------------
NORMAL MODES
------------
These modes are the cartesian displacements weighted by the diagonal matrix
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
Thus, these vectors are normalized but *not* orthogonal
0 1 2 3 4 5
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
11 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
14 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
6 7 8 9 10 11
0 0.096478 0.069838 0.050248 0.000010 0.000019 -0.000055
1 -0.065244 0.108600 -0.025674 -0.000011 0.000021 0.000069
2 -0.056089 -0.006199 0.116297 -0.000008 0.000010 -0.000696
3 0.042224 0.030585 0.022027 0.000012 0.000026 0.500511
4 0.305743 -0.508952 0.120378 0.421773 -0.268725 0.000037
5 0.262927 0.029150 -0.545087 -0.268591 -0.421762 -0.000327
6 -0.446639 -0.356444 -0.016705 0.373142 0.287917 -0.164413
7 0.300443 -0.481324 -0.089851 -0.242470 0.406776 0.157892
8 0.277956 -0.048142 0.037122 -0.227772 0.038608 -0.437685
9 -0.260471 -0.392619 -0.323373 0.062794 -0.467329 -0.168200
10 -0.043851 -0.389729 0.280677 -0.364444 -0.157488 0.306787
11 -0.151661 0.170456 -0.355091 0.336493 -0.083277 0.363261
12 -0.484714 -0.113693 -0.280683 -0.436070 0.179158 -0.167245
13 0.215094 0.085959 -0.005280 0.185271 0.019192 -0.465534
14 0.279111 -0.077600 -0.522699 0.159961 0.466316 0.083050
12 13 14
0 -0.041799 -0.067804 0.034456
1 0.060729 -0.053426 -0.031456
2 0.045783 0.008959 0.073182
3 0.416362 0.672865 -0.337751
4 0.029774 -0.026169 -0.015414
5 0.022464 0.004421 0.035838
6 -0.046171 -0.041860 -0.284313
7 0.054430 -0.017894 0.273820
8 -0.045893 -0.018572 -0.765458
9 0.269741 -0.045258 0.092312
10 -0.499633 -0.004259 -0.152995
11 -0.605082 0.030381 -0.127224
12 -0.141875 0.222181 0.119183
13 -0.308202 0.684923 0.269413
14 0.082978 -0.122986 -0.015165
-----------
IR SPECTRUM
-----------
Mode freq eps Int T**2 TX TY TZ
cm**-1 L/(mol*cm) km/mol a.u.
----------------------------------------------------------------------------
6: 1411.89 0.000735 3.72 0.000163 (-0.001597 -0.008137 -0.009685)
7: 1411.94 0.000436 2.20 0.000096 (-0.001157 -0.003252 0.009192)
8: 1411.99 0.000207 1.05 0.000046 (-0.000833 0.000200 -0.006713)
9: 1567.72 0.001550 7.83 0.000308 (-0.000000 -0.007232 0.016004)
10: 1567.76 0.000015 0.08 0.000003 (-0.000001 -0.000749 0.001567)
11: 2918.15 0.004195 21.20 0.000449 (-0.014320 0.013320 0.008134)
12: 2930.72 0.002517 12.72 0.000268 (-0.011427 0.008458 0.008116)
13: 2930.81 0.006524 32.97 0.000695 (-0.018466 -0.018797 0.000568)
14: 2931.00 0.006335 32.01 0.000674 ( 0.009269 -0.007394 0.023106)
* The epsilon (eps) is given for a Dirac delta lineshape.
** The dipole moment derivative (T) already includes vibrational overlap.
The first frequency considered to be a vibration is 6
The total number of vibrations considered is 9
--------------------------
THERMOCHEMISTRY AT 298.15K
--------------------------
Temperature ... 298.15 K
Pressure ... 1.00 atm
Total Mass ... 16.04 AMU
Throughout the following assumptions are being made:
(1) The electronic state is orbitally nondegenerate
(2) There are no thermally accessible electronically excited states
(3) Hindered rotations indicated by low frequency modes are not
treated as such but are treated as vibrations and this may
cause some error
(4) All equations used are the standard statistical mechanics
equations for an ideal gas
(5) All vibrations are strictly harmonic
freq. 1411.89 E(vib) ... 0.00
freq. 1411.94 E(vib) ... 0.00
freq. 1411.99 E(vib) ... 0.00
freq. 1567.72 E(vib) ... 0.00
freq. 1567.76 E(vib) ... 0.00
freq. 2918.15 E(vib) ... 0.00
freq. 2930.72 E(vib) ... 0.00
freq. 2930.81 E(vib) ... 0.00
freq. 2931.00 E(vib) ... 0.00
------------
INNER ENERGY
------------
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans)
E(el) - is the total energy from the electronic structure calculation
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc)
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation
E(vib) - the the finite temperature correction to E(ZPE) due to population
of excited vibrational states
E(rot) - is the rotational thermal energy
E(trans)- is the translational thermal energy
Summary of contributions to the inner energy U:
Electronic energy ... -4.17445328 Eh
Zero point energy ... 0.04347196 Eh 27.28 kcal/mol
Thermal vibrational correction ... 0.00002868 Eh 0.02 kcal/mol
Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol
-----------------------------------------------------------------------
Total thermal energy -4.12812009 Eh
Summary of corrections to the electronic energy:
(perhaps to be used in another calculation)
Total thermal correction 0.00286122 Eh 1.80 kcal/mol
Non-thermal (ZPE) correction 0.04347196 Eh 27.28 kcal/mol
-----------------------------------------------------------------------
Total correction 0.04633319 Eh 29.07 kcal/mol
--------
ENTHALPY
--------
The enthalpy is H = U + kB*T
kB is Boltzmann's constant
Total free energy ... -4.12812009 Eh
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol
-----------------------------------------------------------------------
Total Enthalpy ... -4.12717588 Eh
Note: Rotational entropy computed according to Herzberg
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945
Point Group: Td, Symmetry Number: 12
Rotational constants in cm-1: 5.186502 5.186421 5.186221
Vibrational entropy computed according to the QRRHO of S. Grimme
Chem.Eur.J. 2012 18 9955
-------
ENTROPY
-------
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans))
S(el) - electronic entropy
S(vib) - vibrational entropy
S(rot) - rotational entropy
S(trans)- translational entropy
The entropies will be listed as multiplied by the temperature to get
units of energy
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol
Vibrational entropy ... 0.00003278 Eh 0.02 kcal/mol
Rotational entropy ... 0.00483337 Eh 3.03 kcal/mol
Translational entropy ... 0.01627961 Eh 10.22 kcal/mol
-----------------------------------------------------------------------
Final entropy term ... 0.02114577 Eh 13.27 kcal/mol
In case the symmetry of your molecule has not been determined correctly
or in case you have a reason to use a different symmetry number we print
out the resulting rotational entropy values for sn=1,12 :
--------------------------------------------------------
| sn= 1 | S(rot)= 0.00717958 Eh 4.51 kcal/mol|
| sn= 2 | S(rot)= 0.00652512 Eh 4.09 kcal/mol|
| sn= 3 | S(rot)= 0.00614229 Eh 3.85 kcal/mol|
| sn= 4 | S(rot)= 0.00587066 Eh 3.68 kcal/mol|
| sn= 5 | S(rot)= 0.00565998 Eh 3.55 kcal/mol|
| sn= 6 | S(rot)= 0.00548783 Eh 3.44 kcal/mol|
| sn= 7 | S(rot)= 0.00534228 Eh 3.35 kcal/mol|
| sn= 8 | S(rot)= 0.00521621 Eh 3.27 kcal/mol|
| sn= 9 | S(rot)= 0.00510500 Eh 3.20 kcal/mol|
| sn=10 | S(rot)= 0.00500552 Eh 3.14 kcal/mol|
| sn=11 | S(rot)= 0.00491553 Eh 3.08 kcal/mol|
| sn=12 | S(rot)= 0.00483337 Eh 3.03 kcal/mol|
--------------------------------------------------------
-------------------
GIBBS FREE ENERGY
-------------------
The Gibbs free energy is G = H - T*S
Total enthalpy ... -4.12717588 Eh
Total entropy correction ... -0.02114577 Eh -13.27 kcal/mol
-----------------------------------------------------------------------
Final Gibbs free energy ... -4.14832165 Eh
For completeness - the Gibbs free energy minus the electronic energy
G-E(el) ... 0.02613163 Eh 16.40 kcal/mol
Timings for individual modules:
Sum of individual times ... 63.124 sec (= 1.052 min)
Numerical frequency calculation ... 63.060 sec (= 1.051 min) 99.9 %
XTB module ... 0.064 sec (= 0.001 min) 0.1 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 1 minutes 3 seconds 189 msec

@ -0,0 +1,7 @@
5
Coordinates from ORCA-job cmmd
C 0.95687316815352 -0.06112204544860 -0.06641298744721
H 2.05652198640884 -0.06109756530571 -0.06634976471074
H 0.59033246206982 0.29086224198130 -1.04156303288977
H 0.59037415480610 0.60741379222750 0.72603912396949
H 0.59032822856172 -1.08163642345449 0.11639666107824

@ -0,0 +1,48 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 16.0430000000
Spin Degeneracy : 1.0000000000
Electronic Energy (Hartree) : -4.1744532782
Translational Energy (Hartree) : 0.0014162714
Rotational Energy (Hartree) : 0.0014162714
Vibrational Energy (Hartree) : 0.0000286783
Number of frequencies : 15
Scaling Factor for frequencies : 1.0000000000
Vibrational frequencies :
0
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1411.894158
7 1411.942387
8 1411.989208
9 1567.724975
10 1567.756664
11 2918.147432
12 2930.722274
13 2930.813685
14 2930.996046
Zero Point Energy (Hartree) : 0.0434719647
Inner Energy (Hartree) : -4.1281200924
Enthalpy (Hartree) : -4.1271758833
Electronic entropy : 0.0000000000
Rotational entropy : 0.0048333747
Vibrational entropy : 0.0000327813
Translational entropy : 0.0048333747
Entropy : 0.0211457665
Gibbs Energy (Hartree) : -4.1483216498
Is Linear : false
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,21 @@
5
Coordinates from ORCA-job cmmd E -40.451784938188
C 0.956890 -0.061120 -0.066380
H 2.049080 -0.061120 -0.066380
H 0.592820 0.288480 -1.034950
H 0.592820 0.602900 0.720670
H 0.592820 -1.074720 0.115150
5
Coordinates from ORCA-job cmmd E -40.451924540961
C 0.956878 -0.061120 -0.066402
H 2.056475 -0.061105 -0.066362
H 0.590353 0.290846 -1.041510
H 0.590377 0.607388 0.725999
H 0.590347 -1.081589 0.116385
5
Coordinates from ORCA-job cmmd E -40.451924547020
C 0.956873 -0.061122 -0.066413
H 2.056522 -0.061098 -0.066350
H 0.590332 0.290862 -1.041563
H 0.590374 0.607414 0.726039
H 0.590328 -1.081636 0.116397

@ -0,0 +1,7 @@
5
XYZ file generated by Avogadro.
C -2.23209 1.11879 -0.00000
H -1.43210 0.87042 0.66574
H -1.90949 1.88312 -0.67574
H -2.51738 0.24944 -0.55475
H -3.06940 1.47217 0.56475

@ -0,0 +1,10 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

@ -0,0 +1,8 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel geom.smi -O geom.xyz --gen3d

@ -0,0 +1,26 @@
#
# Number of atoms
#
3
#
# The current total energy in Eh
#
-10.306829455250
#
# The current gradient in Eh/bohr
#
-0.042660634499
-0.000000000306
0.000000001629
-0.000000242791
0.000000000542
-0.000000002879
0.042660877290
-0.000000000236
0.000000001251
#
# The atomic numbers and current coordinates in Bohr
#
8 2.0516285 0.0008882 0.1843806
6 4.2499940 0.0008882 0.1843806
8 6.4483597 0.0008882 0.1843806

Binary file not shown.

@ -0,0 +1,116 @@
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-10.306829
$hessian
9
0 1 2 3 4
0 1.0172558866E+00 3.7717939410E-10 -2.0158590912E-09 -9.6522099886E-01 -3.3453629031E-10
1 3.7717939410E-10 4.6257550965E-02 7.1422933750E-13 -3.9371313327E-10 -4.8415046700E-02
2 -2.0158590912E-09 7.1422933750E-13 4.6257550963E-02 2.1016768163E-09 -2.8402779435E-12
3 -9.6522099886E-01 -3.9371313327E-10 2.1016768163E-09 1.9304270433E+00 1.2319228909E-10
4 -3.3453629031E-10 -4.8415046700E-02 -2.8402779435E-12 1.2319228909E-10 1.4621391619E-01
5 1.7855160986E-09 6.4867390050E-13 -4.8415046685E-02 -6.5106717659E-10 2.0327540885E-12
6 -5.2027873836E-02 2.2757391073E-13 1.8907040842E-12 -9.6522007231E-01 2.3591578074E-10
7 -2.0432886188E-12 -2.2534365607E-02 2.5381625415E-12 2.6245214419E-10 -4.8415147821E-02
8 1.3193083418E-11 -1.1466340465E-12 -2.2534365615E-02 -1.4073202047E-09 2.9823040150E-13
5 6 7 8
0 1.7855160986E-09 -5.2027873836E-02 -2.0432886188E-12 1.3193083418E-11
1 6.4867390050E-13 2.2757391073E-13 -2.2534365607E-02 -1.1466340465E-12
2 -4.8415046685E-02 1.8907040842E-12 2.5381625415E-12 -2.2534365615E-02
3 -6.5106717659E-10 -9.6522007231E-01 2.6245214419E-10 -1.4073202047E-09
4 2.0327540885E-12 2.3591578074E-10 -4.8415147821E-02 2.9823040150E-13
5 1.4621391619E-01 -1.2654105292E-09 -3.1249372990E-12 -4.8415147827E-02
6 -1.2654105292E-09 1.0172549601E+00 -2.6859343894E-10 1.4374199555E-09
7 -3.1249372990E-12 -2.6859343894E-10 4.6257653100E-02 8.7979902001E-13
8 -4.8415147827E-02 1.4374199555E-09 8.7979902001E-13 4.6257653101E-02
$vibrational_frequencies
9
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 600.703532
6 600.703532
7 1328.912392
8 2416.816551
$normal_modes
9 9
0 1 2 3 4
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
6 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 6 7 8
0 -2.3648407580E-09 -4.6552238897E-10 -7.0710664842E-01 -3.3154792498E-01
1 1.2276547308E-01 -3.0798137360E-01 -2.4533875555E-10 -1.9830812166E-10
2 -3.0798137360E-01 -1.2276547308E-01 1.3121764702E-09 1.0587844555E-09
3 3.0553128916E-10 5.9475780235E-11 -3.5369919662E-07 8.8326227666E-01
4 -3.2705431550E-01 8.2048017898E-01 6.5359681247E-10 5.7884064953E-11
5 8.2048017898E-01 3.2705431550E-01 -3.4957149607E-09 -3.0583792470E-10
6 2.1354678417E-09 4.2087184936E-10 7.0710691395E-01 -3.3154746879E-01
7 1.2276545906E-01 -3.0798133843E-01 -2.4533886896E-10 1.5485256168E-10
8 -3.0798133843E-01 -1.2276545906E-01 1.3121770764E-09 -8.2918139823E-10
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
3
O 15.99900 2.051628489027 0.000888170893 0.184380580973
C 12.01100 4.249993991510 0.000888172063 0.184380574714
O 15.99900 6.448359745030 0.000888170893 0.184380580973
$actual_temperature
0.000000
$frequency_scale_factor
1.000000
$dipole_derivatives
9
-1.4000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 -4.0000000000E-01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 -4.0000000000E-01
3.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 8.0000000000E-01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 8.0000000000E-01
-1.4000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 -4.0000000000E-01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 -4.0000000000E-01
#
# The IR spectrum
# wavenumber eps Int TX TY TZ
#
$ir_spectrum
9
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
600.70 0.01413744 71.44481416 0.000000 -0.031733 0.079608
600.70 0.01413744 71.44481416 0.000000 0.079608 0.031733
1328.91 0.00000000 0.00000000 -0.000000 0.000000 -0.000000
2416.82 0.19163901 968.46501055 0.157305 0.000000 -0.000000
$end

@ -0,0 +1,13 @@
#CMMDE generated Orca input file
!XTB2 Numfreq
%pal
nprocs 1
end
*xyzfile 0 1 cmmd.xyz
%freq
scalfreq 1
Temp 298.15
Pressure 1.0
end

@ -0,0 +1,119 @@
$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
4 9
1.98799189 0.00088817 0.18438058 4.24999408 0.00088817 0.18438058
6.51199626 0.00088817 0.18438058
2.04568896 0.00088817 0.18438058 4.24999407 0.00088817 0.18438058
6.45429920 0.00088817 0.18438058
2.05236544 0.00088817 0.18438058 4.24999403 0.00088817 0.18438057
6.44762275 0.00088817 0.18438058
2.05162112 0.00088817 0.18438058 4.24999366 0.00088817 0.18438057
6.44836745 0.00088817 0.18438058
# redundant internal coordinates
# nbonds nangles ndihedrals nimpropers ncartesians
# bond definitions A B
# angle definitions A B C
# dihedral definitions A B C D
# improper torsion definitions A B C D
# cartesian definitions A x/y/z
$redundant_internals
2 2 0 0 0
1 0 0
2 1 0
0 1 2 -8 0
0 1 2 -4 0
$energies
4
-188.3560728084584639
-188.3604090030537179
-188.3604497811382998
-188.3604503522372795
$gradients
4 9
-0.0660464538439282 0.0000000053304393 0.0000000001716335 0.0000000128165979
0.0000000022640539 0.0000000026807788 0.0660464549296912 -0.0000000161230601
-0.0000000078716251
-0.0068505804958569 0.0000000053495906 -0.0000000149072329 0.0000001199697298
-0.0000000003533555 -0.0000000010682996 0.0068504632637335 0.0000000035999274
0.0000000055705466
0.0008590760165977 0.0000000043006531 -0.0000000143543937 0.0000014546664970
0.0000000003891685 -0.0000000038394442 -0.0008605282115356 0.0000000010853741
0.0000000041938126
-0.0000082136982629 0.0000000047182270 -0.0000000144218323 -0.0000011585474631
0.0000000026750576 -0.0000000057815938 0.0000093738124540 0.0000000018118397
0.0000000052452088
$redundant_coords
4 4
2.2620021823037382 2.2620021823037373 3.1415926535897931 3.1415926535897931
2.2043051168065126 2.2043051239545850 3.1415926535897931 3.1415926535897931
2.1976285904240038 2.1976287143764415 3.1415926535897931 3.1415926535897931
2.1983725358524921 2.1983737944425048 3.1415926535897931 3.1415926535897931
$redundant_gradients
4 4
0.0660464584780485 0.0660464502955709 0.0000000025534548 -0.0000000021769249
0.0068505814083924 0.0068504623511980 -0.0000000015947643 -0.0000000012124678
-0.0008590751927447 -0.0008605290353886 -0.0000000007682665 -0.0000000004112485
0.0000082142205056 0.0000093732902113 -0.0000000001966618 0.0000000003977327
$hessian_approx
9 9
0 1 2 3 4 5
0 1.150980 -0.000000 0.000000 -1.136192 -0.000002 0.000001
1 -0.000000 0.535644 -0.000000 -0.000000 -1.071288 -0.000000
2 0.000000 -0.000000 0.535644 0.000000 -0.000000 -1.071288
3 -1.136192 -0.000000 0.000000 2.274183 -0.000000 0.000000
4 -0.000002 -1.071288 -0.000000 -0.000000 2.142575 -0.000000
5 0.000001 -0.000000 -1.071288 0.000000 -0.000000 2.142575
6 -0.014788 0.000000 -0.000000 -1.137992 0.000002 -0.000001
7 -0.000000 0.535644 -0.000000 -0.000000 -1.071288 -0.000000
8 -0.000001 0.000000 0.535644 -0.000000 0.000000 -1.071288
6 7 8
0 -0.014788 -0.000000 -0.000001
1 0.000000 0.535644 0.000000
2 -0.000000 -0.000000 0.535644
3 -1.137992 -0.000000 -0.000000
4 0.000002 -1.071288 0.000000
5 -0.000001 -0.000000 -1.071288
6 1.152778 0.000000 0.000001
7 0.000000 0.535644 0.000000
8 0.000001 0.000000 0.535644
$bmatrix
4 9
0 1 2 3 4 5
0 -1.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000
1 0.000000 0.000000 0.000000 -1.000000 0.000000 -0.000000
2 0.000000 -1.000000 0.000000 -0.000000 2.000000 -0.000000
3 0.000000 -0.000000 1.000000 -0.000000 0.000000 -2.000000
6 7 8
0 0.000000 0.000000 0.000000
1 1.000000 -0.000000 0.000000
2 -0.000000 -1.000000 0.000000
3 -0.000000 0.000000 1.000000

@ -0,0 +1,647 @@
*****************
* O R C A *
*****************
#,
###
####
#####
######
########,
,,################,,,,,
,,#################################,,
,,##########################################,,
,#########################################, ''#####,
,#############################################,, '####,
,##################################################,,,,####,
,###########'''' ''''###############################
,#####'' ,,,,##########,,,, '''####''' '####
,##' ,,,,###########################,,, '##
' ,,###'''' '''############,,,
,,##'' '''############,,,, ,,,,,,###''
,#'' '''#######################'''
' ''''####''''
,#######, #######, ,#######, ##
,#' '#, ## ## ,#' '#, #''# ###### ,####,
## ## ## ,#' ## #' '# # #' '#
## ## ####### ## ,######, #####, # #
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,#
'#######' ## ## '#######' #' '# #####' # '####'
#######################################################
# -***- #
# Department of theory and spectroscopy #
# Directorship and core code : Frank Neese #
# Max Planck Institute fuer Kohlenforschung #
# Kaiser Wilhelm Platz 1 #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 5.0.2 - RELEASE -
With contributions from (in alphabetic order):
Daniel Aravena : Magnetic Suceptibility
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation)
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum
Ute Becker : Parallelization
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD
Martin Brehm : Molecular dynamics
Dmytro Bykov : SCF Hessian
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE
Dipayan Datta : RHF DLPNO-CCSD density
Achintya Kumar Dutta : EOM-CC, STEOM-CC
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
Lee Huntington : MR-EOM, pCC
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
Marcus Kettner : VPT2
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
Martin Krupicka : Initial AUTO-CI
Lucas Lang : DCDCAS
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC
Dagmar Lenk : GEPOL surface, SMD
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization
Dimitrios Manganas : Further ROCIS development; embedding schemes
Dimitrios Pantazis : SARC Basis sets
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient
Christoph Reimann : Effective Core Potentials
Marius Retegan : Local ZFS, SOC
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB
Michael Roemelt : Original ROCIS implementation
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density
Barbara Sandhoefer : DKH picture change effects
Avijit Sen : IP-ROCIS
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
Bernardo de Souza : ESD, SOC TD-DFT
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
Willem Van den Heuvel : Paramagnetic NMR
Boris Wezisla : Elementary symmetry handling
Frank Wennmohs : Technical directorship
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization,
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Jiri Pittner, Ondrej Demel : Mk-CCSD
Frank Weinhold : gennbo (NPA and NBO analysis)
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
Lars Goerigk : TD-DFT with DH, B97 family of functionals
V. Asgeirsson, H. Jonsson : NEB implementation
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
nearIR, NL-DFT gradient (VV10), updates on ESD,
ML-optimized integration grids
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library
Liviu Ungur et al : ANISO software
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
Your ORCA version has been built with support for libXC version: 5.1.0
For citations please refer to: https://tddft.org/programs/libxc/
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
SCALAPACK package : Parallel linear algebra routines
Shared memory : Shared parallel matrices
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
Core in use : SkylakeX
Copyright (c) 2011-2014, The OpenBLAS Project
***************************************
The coordinates will be read from file: cmmd.xyz
***************************************
Your calculation utilizes the semiempirical GFN2-xTB method
Please cite in your paper:
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652.
================================================================================
================================================================================
WARNINGS
Please study these warnings very carefully!
================================================================================
WARNING: Old DensityContainer found on disk!
Will remove this file -
If you want to keep old densities, please start your calculation with a different basename.
WARNING: Gradients needed for Numerical Frequencies
===> : Setting RunTyp to EnGrad
WARNING: Found dipole moment calculation with XTB calculation
===> : Switching off dipole moment calculation
WARNING: TRAH-SCF for XTB is not implemented!
===> : Turning TRAH off!
================================================================================
INPUT FILE
================================================================================
NAME = cmmd.in
| 1> #CMMDE generated Orca input file
| 2> !XTB2 Numfreq
| 3> %pal
| 4> nprocs 1
| 5> end
| 6>
| 7> *xyzfile 0 1 cmmd.xyz
| 8>
| 9> %freq
| 10> scalfreq 1
| 11> Temp 298.15
| 12> Pressure 1.0
| 13> end
| 14>
| 15> ****END OF INPUT****
================================================================================
*******************************
* Energy+Gradient Calculation *
*******************************
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/04/28 at 11:27:29.719
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 3
number of electrons : 16
charge : 0
spin : 0.0
first test random number : 0.68590959901946
ID Z sym. atoms
1 8 O 1, 3
2 6 C 2
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
...................................................
: SETUP :
:.................................................:
: # basis functions 12 :
: # atomic orbitals 12 :
: # shells 6 :
: # electrons 16 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -10.3965360 -0.103965E+02 0.837E+00 8.67 0.0 T
2 -10.4101892 -0.136532E-01 0.431E+00 7.88 1.0 T
3 -10.4094776 0.711590E-03 0.204E+00 8.23 1.0 T
4 -10.4117031 -0.222544E-02 0.655E-02 7.98 1.0 T
5 -10.4117158 -0.127551E-04 0.707E-03 8.00 8.2 T
6 -10.4117158 -0.371099E-09 0.255E-03 7.99 22.6 T
7 -10.4117158 -0.126620E-07 0.789E-05 7.99 731.6 T
8 -10.4117158 0.113864E-11 0.304E-05 7.99 1897.3 T
*** convergence criteria satisfied after 8 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.8071320 -21.9632
2 2.0000 -0.7942628 -21.6130
3 2.0000 -0.6642345 -18.0747
4 2.0000 -0.6586945 -17.9240
5 2.0000 -0.6586945 -17.9240
6 2.0000 -0.6017795 -16.3753
7 2.0000 -0.5339897 -14.5306
8 2.0000 -0.5339897 -14.5306 (HOMO)
9 -0.2401980 -6.5361 (LUMO)
10 -0.2401980 -6.5361
11 0.2460866 6.6964
12 1.2242558 33.3137
-------------------------------------------------------------
HL-Gap 0.2937917 Eh 7.9945 eV
Fermi-level -0.3870939 Eh -10.5334 eV
SCC (total) 0 d, 0 h, 0 min, 0.008 sec
SCC setup ... 0 min, 0.000 sec ( 0.895%)
Dispersion ... 0 min, 0.000 sec ( 0.159%)
classical contributions ... 0 min, 0.000 sec ( 0.101%)
integral evaluation ... 0 min, 0.000 sec ( 2.187%)
iterations ... 0 min, 0.008 sec ( 90.726%)
molecular gradient ... 0 min, 0.000 sec ( 3.490%)
printout ... 0 min, 0.000 sec ( 2.293%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -10.306829455248 Eh ::
:: gradient norm 0.060331419568 Eh/a0 ::
:: HOMO-LUMO gap 7.994478852059 eV ::
::.................................................::
:: SCC energy -10.411715834534 Eh ::
:: -> isotropic ES 0.032208314694 Eh ::
:: -> anisotropic ES 0.003353522512 Eh ::
:: -> anisotropic XC 0.000791903701 Eh ::
:: -> dispersion -0.000686207603 Eh ::
:: repulsion energy 0.104886381085 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -10.306829455248 Eh |
| GRADIENT NORM 0.060331419568 Eh/α |
| HOMO-LUMO GAP 7.994478852059 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/04/28 at 11:27:29.735
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.016 sec
* cpu-time: 0 d, 0 h, 0 min, 0.010 sec
* ratio c/w: 0.598 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.009 sec
* cpu-time: 0 d, 0 h, 0 min, 0.002 sec
* ratio c/w: 0.249 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -10.306829455250
------------------------- --------------------
----------------------------------------------------------------------------
ORCA NUMERICAL FREQUENCIES
----------------------------------------------------------------------------
Number of atoms ... 3
Central differences ... used
Number of displacements ... 18
Numerical increment ... 5.000e-03 bohr
IR-spectrum generation ... on
Raman-spectrum generation ... off
Surface Crossing Hessian ... off
The output will be reduced. Please look at the following files:
SCF program output ... >cmmd.lastscf
Integral program output ... >cmmd.lastint
Gradient program output ... >cmmd.lastgrad
Dipole moment program output ... >cmmd.lastmom
AutoCI program output ... >cmmd.lastautoci
<< Calculating on displaced geometry 1 (of 18) >>
<< Calculating on displaced geometry 2 (of 18) >>
<< Calculating on displaced geometry 3 (of 18) >>
<< Calculating on displaced geometry 4 (of 18) >>
<< Calculating on displaced geometry 5 (of 18) >>
<< Calculating on displaced geometry 6 (of 18) >>
<< Calculating on displaced geometry 7 (of 18) >>
<< Calculating on displaced geometry 8 (of 18) >>
<< Calculating on displaced geometry 9 (of 18) >>
<< Calculating on displaced geometry 10 (of 18) >>
<< Calculating on displaced geometry 11 (of 18) >>
<< Calculating on displaced geometry 12 (of 18) >>
<< Calculating on displaced geometry 13 (of 18) >>
<< Calculating on displaced geometry 14 (of 18) >>
<< Calculating on displaced geometry 15 (of 18) >>
<< Calculating on displaced geometry 16 (of 18) >>
<< Calculating on displaced geometry 17 (of 18) >>
<< Calculating on displaced geometry 18 (of 18) >>
-----------------------
VIBRATIONAL FREQUENCIES
-----------------------
Scaling factor for frequencies = 1.000000000 (already applied!)
0: 0.00 cm**-1
1: 0.00 cm**-1
2: 0.00 cm**-1
3: 0.00 cm**-1
4: 0.00 cm**-1
5: 600.70 cm**-1
6: 600.70 cm**-1
7: 1328.91 cm**-1
8: 2416.82 cm**-1
------------
NORMAL MODES
------------
These modes are the cartesian displacements weighted by the diagonal matrix
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
Thus, these vectors are normalized but *not* orthogonal
0 1 2 3 4 5
0 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.122765
2 0.000000 0.000000 0.000000 0.000000 0.000000 -0.307981
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 0.000000 0.000000 -0.327054
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.820480
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.000000 0.000000 0.000000 0.000000 0.000000 0.122765
8 0.000000 0.000000 0.000000 0.000000 0.000000 -0.307981
6 7 8
0 -0.000000 -0.707107 -0.331548
1 -0.307981 -0.000000 -0.000000
2 -0.122765 0.000000 0.000000
3 0.000000 -0.000000 0.883262
4 0.820480 0.000000 0.000000
5 0.327054 -0.000000 -0.000000
6 0.000000 0.707107 -0.331547
7 -0.307981 -0.000000 0.000000
8 -0.122765 0.000000 -0.000000
-----------
IR SPECTRUM
-----------
Mode freq eps Int T**2 TX TY TZ
cm**-1 L/(mol*cm) km/mol a.u.
----------------------------------------------------------------------------
5: 600.70 0.014137 71.44 0.007344 ( 0.000000 -0.031733 0.079608)
6: 600.70 0.014137 71.44 0.007344 ( 0.000000 0.079608 0.031733)
7: 1328.91 0.000000 0.00 0.000000 (-0.000000 0.000000 -0.000000)
8: 2416.82 0.191639 968.47 0.024745 ( 0.157305 0.000000 -0.000000)
* The epsilon (eps) is given for a Dirac delta lineshape.
** The dipole moment derivative (T) already includes vibrational overlap.
The first frequency considered to be a vibration is 5
The total number of vibrations considered is 4
--------------------------
THERMOCHEMISTRY AT 298.15K
--------------------------
Temperature ... 298.15 K
Pressure ... 1.00 atm
Total Mass ... 44.01 AMU
The molecule is recognized as being linear
Throughout the following assumptions are being made:
(1) The electronic state is orbitally nondegenerate
(2) There are no thermally accessible electronically excited states
(3) Hindered rotations indicated by low frequency modes are not
treated as such but are treated as vibrations and this may
cause some error
(4) All equations used are the standard statistical mechanics
equations for an ideal gas
(5) All vibrations are strictly harmonic
freq. 600.70 E(vib) ... 0.10
freq. 600.70 E(vib) ... 0.10
freq. 1328.91 E(vib) ... 0.01
freq. 2416.82 E(vib) ... 0.00
------------
INNER ENERGY
------------
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans)
E(el) - is the total energy from the electronic structure calculation
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc)
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation
E(vib) - the the finite temperature correction to E(ZPE) due to population
of excited vibrational states
E(rot) - is the rotational thermal energy
E(trans)- is the translational thermal energy
Summary of contributions to the inner energy U:
Electronic energy ... -10.30682946 Eh
Zero point energy ... 0.01127041 Eh 7.07 kcal/mol
Thermal vibrational correction ... 0.00032921 Eh 0.21 kcal/mol
Thermal rotational correction ... 0.00094418 Eh 0.59 kcal/mol
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol
-----------------------------------------------------------------------
Total thermal energy -10.29286939 Eh
Summary of corrections to the electronic energy:
(perhaps to be used in another calculation)
Total thermal correction 0.00268966 Eh 1.69 kcal/mol
Non-thermal (ZPE) correction 0.01127041 Eh 7.07 kcal/mol
-----------------------------------------------------------------------
Total correction 0.01396007 Eh 8.76 kcal/mol
--------
ENTHALPY
--------
The enthalpy is H = U + kB*T
kB is Boltzmann's constant
Total free energy ... -10.29286939 Eh
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol
-----------------------------------------------------------------------
Total Enthalpy ... -10.29192518 Eh
Note: Rotational entropy computed according to Herzberg
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945
Point Group: Dinfh, Symmetry Number: 2
Rotational constants in cm-1: 0.000000 0.389289 0.389289
Vibrational entropy computed according to the QRRHO of S. Grimme
Chem.Eur.J. 2012 18 9955
-------
ENTROPY
-------
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans))
S(el) - electronic entropy
S(vib) - vibrational entropy
S(rot) - rotational entropy
S(trans)- translational entropy
The entropies will be listed as multiplied by the temperature to get
units of energy
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol
Vibrational entropy ... 0.00043823 Eh 0.27 kcal/mol
Rotational entropy ... 0.00621658 Eh 3.90 kcal/mol
Translational entropy ... 0.01770880 Eh 11.11 kcal/mol
-----------------------------------------------------------------------
Final entropy term ... 0.02436361 Eh 15.29 kcal/mol
-------------------
GIBBS FREE ENERGY
-------------------
The Gibbs free energy is G = H - T*S
Total enthalpy ... -10.29192518 Eh
Total entropy correction ... -0.02436361 Eh -15.29 kcal/mol
-----------------------------------------------------------------------
Final Gibbs free energy ... -10.31628879 Eh
For completeness - the Gibbs free energy minus the electronic energy
G-E(el) ... -0.00945933 Eh -5.94 kcal/mol
Timings for individual modules:
Sum of individual times ... 44.986 sec (= 0.750 min)
Numerical frequency calculation ... 44.913 sec (= 0.749 min) 99.8 %
XTB module ... 0.073 sec (= 0.001 min) 0.2 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 44 seconds 988 msec

@ -0,0 +1,5 @@
3
Coordinates from ORCA-job cmmd
O 1.08567503629188 0.00046999979347 0.09757000110407
C 2.24899995571885 0.00047000041305 0.09756999779185
O 3.41232500798927 0.00046999979347 0.09757000110407

@ -0,0 +1,42 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 44.0090000000
Spin Degeneracy : 1.0000000000
Electronic Energy (Hartree) : -10.3068294552
Translational Energy (Hartree) : 0.0014162714
Rotational Energy (Hartree) : 0.0009441809
Vibrational Energy (Hartree) : 0.0003292089
Number of frequencies : 9
Scaling Factor for frequencies : 1.0000000000
Vibrational frequencies :
0
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 600.703532
6 600.703532
7 1328.912392
8 2416.816551
Zero Point Energy (Hartree) : 0.0112704051
Inner Energy (Hartree) : -10.2928693888
Enthalpy (Hartree) : -10.2919251798
Electronic entropy : 0.0000000000
Rotational entropy : 0.0062165785
Vibrational entropy : 0.0004382285
Translational entropy : 0.0062165785
Entropy : 0.0243636075
Gibbs Energy (Hartree) : -10.3162887873
Is Linear : false
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,25 @@
3
Coordinates from ORCA-job cmmd E -188.356072808458
O 1.052000 0.000470 0.097570
C 2.249000 0.000470 0.097570
O 3.446000 0.000470 0.097570
3
Coordinates from ORCA-job cmmd E -188.360409003054
O 1.082532 0.000470 0.097570
C 2.249000 0.000470 0.097570
O 3.415468 0.000470 0.097570
3
Coordinates from ORCA-job cmmd E -188.360449781138
O 1.086065 0.000470 0.097570
C 2.249000 0.000470 0.097570
O 3.411935 0.000470 0.097570
3
Coordinates from ORCA-job cmmd E -188.360450352237
O 1.085671 0.000470 0.097570
C 2.249000 0.000470 0.097570
O 3.412329 0.000470 0.097570
3
Coordinates from ORCA-job cmmd E -188.360450353656
O 1.085675 0.000470 0.097570
C 2.249000 0.000470 0.097570
O 3.412325 0.000470 0.097570

@ -0,0 +1,5 @@
3
O 1.05200 0.00047 0.09757
C 2.24900 0.00047 0.09757
O 3.44600 0.00047 0.09757

@ -0,0 +1,10 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

@ -0,0 +1,8 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel geom.smi -O geom.xyz --gen3d

@ -0,0 +1,26 @@
#
# Number of atoms
#
3
#
# The current total energy in Eh
#
-5.070123981300
#
# The current gradient in Eh/bohr
#
-0.008377591894
-0.009332836846
-0.007297711124
0.004688751138
0.004388014404
0.003431157867
0.003688840756
0.004944822442
0.003866553256
#
# The atomic numbers and current coordinates in Bohr
#
8 1.7463773 0.0986767 -0.0997319
1 3.5707559 0.1789166 -0.0369954
1 1.2342827 1.4804000 0.9806980

Binary file not shown.

@ -0,0 +1,116 @@
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-5.070124
$hessian
9
0 1 2 3 4
0 5.0153331710E-01 -5.3060722768E-02 -4.1491079430E-02 -4.3244534659E-01 -4.0084092878E-02
1 -5.3060722768E-02 2.8650738494E-01 2.1405136245E-01 -8.0486957880E-03 -3.0519687256E-02
2 -4.1491079430E-02 2.1405136245E-01 1.8013792250E-01 -6.2920646425E-03 -1.8871513419E-02
3 -4.3244534659E-01 -8.0486957880E-03 -6.2920646425E-03 4.5189264359E-01 3.9039242588E-03
4 -4.0084092878E-02 -3.0519687256E-02 -1.8871513419E-02 3.9039242588E-03 3.0226919572E-02
5 -3.1341920012E-02 -1.8871689535E-02 -2.1141829960E-02 3.0510466469E-03 2.0971324760E-02
6 -6.9088148033E-02 6.1109394648E-02 4.7783125377E-02 -1.9447166108E-02 3.6180182740E-02
7 9.3144650593E-02 -2.5598799181E-01 -1.9517992292E-01 4.1448060830E-03 2.9290278726E-04
8 7.2832797380E-02 -1.9517987280E-01 -1.5899626281E-01 3.2410666038E-03 -2.0996758124E-03
5 6 7 8
0 -3.1341920012E-02 -6.9088148033E-02 9.3144650593E-02 7.2832797380E-02
1 -1.8871689535E-02 6.1109394648E-02 -2.5598799181E-01 -1.9517987280E-01
2 -2.1141829960E-02 4.7783125377E-02 -1.9517992292E-01 -1.5899626281E-01
3 3.0510466469E-03 -1.9447166108E-02 4.1448060830E-03 3.2410666038E-03
4 2.0971324760E-02 3.6180182740E-02 2.9290278726E-04 -2.0996758124E-03
5 1.9805805652E-02 2.8290884407E-02 -2.0995584766E-03 1.3360988061E-03
6 2.8290884407E-02 8.8535360763E-02 -9.7289446888E-02 -7.6073856331E-02
7 -2.0995584766E-03 -9.7289446888E-02 2.5569524804E-01 1.9727954575E-01
8 1.3360988061E-03 -7.6073856331E-02 1.9727954575E-01 1.5766025977E-01
$vibrational_frequencies
9
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1591.021914
7 3532.222317
8 3553.964928
$normal_modes
9 9
0 1 2 3 4
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
6 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 6 7 8
0 0.0000000000E+00 4.0721137498E-02 -5.6762076790E-02 -2.9045170495E-02
1 0.0000000000E+00 4.5365698453E-02 3.1729345277E-02 -3.2146768540E-02
2 0.0000000000E+00 3.5473218659E-02 2.4810723522E-02 -2.5136818297E-02
3 0.0000000000E+00 2.7274520573E-02 7.0266957076E-01 7.0767482621E-01
4 0.0000000000E+00 -5.5522727783E-01 3.0998203060E-02 -9.7397068783E-03
5 0.0000000000E+00 -4.3415585773E-01 2.4236302572E-02 -7.6184151067E-03
6 0.0000000000E+00 -6.7360138449E-01 1.9825946352E-01 -2.4666918856E-01
7 0.0000000000E+00 -1.6481816815E-01 -5.3460712676E-01 5.1997398255E-01
8 0.0000000000E+00 -1.2887591343E-01 -4.1803269704E-01 4.0659059361E-01
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
3
O 15.99900 1.746377337196 0.098676688290 -0.099731938722
H 1.00800 3.570755883853 0.178916624800 -0.036995438538
H 1.00800 1.234282723597 1.480400012035 0.980697965930
$actual_temperature
0.000000
$frequency_scale_factor
1.000000
$dipole_derivatives
9
-4.0000000000E-01 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 -6.0000000000E-01 2.0000000000E-01
0.0000000000E+00 2.0000000000E-01 -6.0000000000E-01
1.0000000000E-01 0.0000000000E+00 0.0000000000E+00
-1.0000000000E-01 4.0000000000E-01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 4.0000000000E-01
3.0000000000E-01 0.0000000000E+00 0.0000000000E+00
1.0000000000E-01 2.0000000000E-01 -2.0000000000E-01
1.0000000000E-01 -2.0000000000E-01 3.0000000000E-01
#
# The IR spectrum
# wavenumber eps Int TX TY TZ
#
$ir_spectrum
9
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
1591.02 0.02402202 121.39743181 -0.035425 -0.046627 -0.035815
3532.22 0.00068734 3.47355421 0.006792 -0.003138 -0.002177
3553.96 0.00222411 11.23974807 0.012984 0.004205 0.003002
$end

@ -0,0 +1,13 @@
#CMMDE generated Orca input file
!XTB2 Numfreq
%pal
nprocs 1
end
*xyzfile 0 1 cmmd.xyz
%freq
scalfreq 1
Temp 298.15
Pressure 1.0
end

@ -0,0 +1,108 @@
$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
4 9
1.74977302 0.10246095 -0.09677288 3.57882004 0.17158713 -0.04272671
1.22282288 1.48394524 0.98347017
1.74856683 0.10111637 -0.09782426 3.57219877 0.17628338 -0.03905449
1.23065035 1.48059358 0.98084934
1.74723144 0.09962851 -0.09898768 3.57099818 0.17806796 -0.03765905
1.23318633 1.48029686 0.98061731
1.74638369 0.09868381 -0.09972637 3.57071543 0.17893384 -0.03698198
1.23431682 1.48037568 0.98067894
# redundant internal coordinates
# nbonds nangles ndihedrals nimpropers ncartesians
# bond definitions A B
# angle definitions A B C
# dihedral definitions A B C D
# improper torsion definitions A B C D
# cartesian definitions A x/y/z
$redundant_internals
2 1 0 0 0
1 0 0
2 0 0
1 0 2 0 0
$energies
4
-76.3212379100696410
-76.3212655904724357
-76.3212690328680594
-76.3212696812114473
$gradients
4 9
-0.0004253922326744 -0.0005001819868337 -0.0003303905934972 0.0025973903065613
-0.0010880141228024 -0.0008601520349792 -0.0021667166814798 0.0015671654932914
0.0012271009412793
0.0007834186175729 0.0008428236020004 0.0007251027461325 -0.0003236165648111
-0.0004686022216160 -0.0003758718456999 -0.0004517894639538 -0.0003950351543238
-0.0003081717188155
0.0003983757946074 0.0004127842267320 0.0003916383200292 -0.0002984982162071
-0.0001614364453191 -0.0001357999461145 -0.0000926555729789 -0.0002736661866776
-0.0002137094933613
0.0000160541345634 -0.0000138278483816 0.0000596139427747 -0.0000255751549404
0.0000054195140033 -0.0000054104954291 0.0000159365342492 -0.0000150225127057
-0.0000117004532667
$redundant_coords
4 3
1.8311505801026724 1.8311472707494942 1.8147573140807562
1.8261263372240049 1.8261247413604469 1.8060846250815792
1.8264827030928774 1.8264814331491046 1.8015498668250125
1.8271735622382301 1.8271728309768116 1.7990716639809692
$redundant_gradients
4 3
0.0025276445547656 0.0025267987700943 0.0027615881197076
-0.0003558507824992 -0.0003559310471405 0.0010632671904284
-0.0003105383757455 -0.0003106763198600 0.0003530776201266
-0.0000261697488893 -0.0000262085824290 -0.0000064837205582
$hessian_approx
9 9
0 1 2 3 4 5
0 0.572190 -0.058342 -0.045804 -0.500828 -0.043281 -0.033824
1 -0.058342 0.322567 0.252024 -0.017583 -0.027909 -0.021805
2 -0.045804 0.252024 0.196912 -0.014064 -0.021494 -0.016793
3 -0.500828 -0.017583 -0.014064 0.530290 0.002073 0.001620
4 -0.043281 -0.027909 -0.021494 0.002073 0.030371 0.023734
5 -0.033824 -0.021805 -0.016793 0.001620 0.023734 0.018548
6 -0.071094 0.076223 0.060101 -0.029696 0.041115 0.032133
7 0.101880 -0.294370 -0.230307 0.015444 -0.002639 -0.002068
8 0.079687 -0.230155 -0.180068 0.012133 -0.002116 -0.001658
6 7 8
0 -0.071094 0.101880 0.079687
1 0.076223 -0.294370 -0.230155
2 0.060101 -0.230307 -0.180068
3 -0.029696 0.015444 0.012133
4 0.041115 -0.002639 -0.002116
5 0.032133 -0.002068 -0.001658
6 0.100758 -0.117528 -0.091982
7 -0.117528 0.296901 0.232186
8 -0.091982 0.232186 0.181576
$bmatrix
3 9
0 1 2 3 4 5
0 -0.998445 -0.043920 -0.034340 0.998445 0.043920 0.034340
1 0.280251 -0.756191 -0.591299 0.000000 0.000000 0.000000
2 0.494849 0.551292 0.431077 0.030512 -0.430465 -0.336599
6 7 8
0 0.000000 0.000000 0.000000
1 -0.280251 0.756191 0.591299
2 -0.525362 -0.120827 -0.094478

@ -0,0 +1,657 @@
*****************
* O R C A *
*****************
#,
###
####
#####
######
########,
,,################,,,,,
,,#################################,,
,,##########################################,,
,#########################################, ''#####,
,#############################################,, '####,
,##################################################,,,,####,
,###########'''' ''''###############################
,#####'' ,,,,##########,,,, '''####''' '####
,##' ,,,,###########################,,, '##
' ,,###'''' '''############,,,
,,##'' '''############,,,, ,,,,,,###''
,#'' '''#######################'''
' ''''####''''
,#######, #######, ,#######, ##
,#' '#, ## ## ,#' '#, #''# ###### ,####,
## ## ## ,#' ## #' '# # #' '#
## ## ####### ## ,######, #####, # #
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,#
'#######' ## ## '#######' #' '# #####' # '####'
#######################################################
# -***- #
# Department of theory and spectroscopy #
# Directorship and core code : Frank Neese #
# Max Planck Institute fuer Kohlenforschung #
# Kaiser Wilhelm Platz 1 #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 5.0.2 - RELEASE -
With contributions from (in alphabetic order):
Daniel Aravena : Magnetic Suceptibility
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation)
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum
Ute Becker : Parallelization
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD
Martin Brehm : Molecular dynamics
Dmytro Bykov : SCF Hessian
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE
Dipayan Datta : RHF DLPNO-CCSD density
Achintya Kumar Dutta : EOM-CC, STEOM-CC
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
Lee Huntington : MR-EOM, pCC
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
Marcus Kettner : VPT2
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
Martin Krupicka : Initial AUTO-CI
Lucas Lang : DCDCAS
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC
Dagmar Lenk : GEPOL surface, SMD
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization
Dimitrios Manganas : Further ROCIS development; embedding schemes
Dimitrios Pantazis : SARC Basis sets
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient
Christoph Reimann : Effective Core Potentials
Marius Retegan : Local ZFS, SOC
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB
Michael Roemelt : Original ROCIS implementation
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density
Barbara Sandhoefer : DKH picture change effects
Avijit Sen : IP-ROCIS
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
Bernardo de Souza : ESD, SOC TD-DFT
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
Willem Van den Heuvel : Paramagnetic NMR
Boris Wezisla : Elementary symmetry handling
Frank Wennmohs : Technical directorship
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization,
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Jiri Pittner, Ondrej Demel : Mk-CCSD
Frank Weinhold : gennbo (NPA and NBO analysis)
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
Lars Goerigk : TD-DFT with DH, B97 family of functionals
V. Asgeirsson, H. Jonsson : NEB implementation
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
nearIR, NL-DFT gradient (VV10), updates on ESD,
ML-optimized integration grids
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library
Liviu Ungur et al : ANISO software
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
Your ORCA version has been built with support for libXC version: 5.1.0
For citations please refer to: https://tddft.org/programs/libxc/
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
SCALAPACK package : Parallel linear algebra routines
Shared memory : Shared parallel matrices
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
Core in use : SkylakeX
Copyright (c) 2011-2014, The OpenBLAS Project
***************************************
The coordinates will be read from file: cmmd.xyz
***************************************
Your calculation utilizes the semiempirical GFN2-xTB method
Please cite in your paper:
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652.
================================================================================
================================================================================
WARNINGS
Please study these warnings very carefully!
================================================================================
WARNING: Old DensityContainer found on disk!
Will remove this file -
If you want to keep old densities, please start your calculation with a different basename.
WARNING: Gradients needed for Numerical Frequencies
===> : Setting RunTyp to EnGrad
WARNING: Found dipole moment calculation with XTB calculation
===> : Switching off dipole moment calculation
WARNING: TRAH-SCF for XTB is not implemented!
===> : Turning TRAH off!
================================================================================
INPUT FILE
================================================================================
NAME = cmmd.in
| 1> #CMMDE generated Orca input file
| 2> !XTB2 Numfreq
| 3> %pal
| 4> nprocs 1
| 5> end
| 6>
| 7> *xyzfile 0 1 cmmd.xyz
| 8>
| 9> %freq
| 10> scalfreq 1
| 11> Temp 298.15
| 12> Pressure 1.0
| 13> end
| 14>
| 15> ****END OF INPUT****
================================================================================
*******************************
* Energy+Gradient Calculation *
*******************************
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/04/28 at 11:27:34.587
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 3
number of electrons : 8
charge : 0
spin : 0.0
first test random number : 0.93951341933391
ID Z sym. atoms
1 8 O 1
2 1 H 2, 3
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
...................................................
: SETUP :
:.................................................:
: # basis functions 6 :
: # atomic orbitals 6 :
: # shells 4 :
: # electrons 8 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -5.1005103 -0.510051E+01 0.419E+00 14.71 0.0 T
2 -5.1019252 -0.141483E-02 0.240E+00 14.41 1.0 T
3 -5.1021667 -0.241498E-03 0.391E-01 14.18 1.0 T
4 -5.1022308 -0.641084E-04 0.843E-02 14.33 1.0 T
5 -5.1022332 -0.246222E-05 0.551E-02 14.28 1.0 T
6 -5.1022352 -0.194708E-05 0.107E-03 14.30 54.1 T
7 -5.1022352 0.126747E-09 0.102E-03 14.30 56.4 T
8 -5.1022352 -0.665856E-09 0.201E-05 14.30 2872.0 T
9 -5.1022352 -0.251354E-12 0.108E-07 14.30 100000.0 T
*** convergence criteria satisfied after 9 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.6809644 -18.5300
2 2.0000 -0.5645561 -15.3624
3 2.0000 -0.5163314 -14.0501
4 2.0000 -0.4474968 -12.1770 (HOMO)
5 0.0780978 2.1251 (LUMO)
6 0.2232972 6.0762
-------------------------------------------------------------
HL-Gap 0.5255946 Eh 14.3022 eV
Fermi-level -0.1846995 Eh -5.0259 eV
SCC (total) 0 d, 0 h, 0 min, 0.033 sec
SCC setup ... 0 min, 0.000 sec ( 0.138%)
Dispersion ... 0 min, 0.000 sec ( 0.017%)
classical contributions ... 0 min, 0.000 sec ( 0.015%)
integral evaluation ... 0 min, 0.000 sec ( 0.149%)
iterations ... 0 min, 0.033 sec ( 99.151%)
molecular gradient ... 0 min, 0.000 sec ( 0.289%)
printout ... 0 min, 0.000 sec ( 0.225%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -5.070123981303 Eh ::
:: gradient norm 0.017792229436 Eh/a0 ::
:: HOMO-LUMO gap 14.302156491823 eV ::
::.................................................::
:: SCC energy -5.102235193405 Eh ::
:: -> isotropic ES 0.031392635975 Eh ::
:: -> anisotropic ES 0.000754364857 Eh ::
:: -> anisotropic XC -0.000693407516 Eh ::
:: -> dispersion -0.000141490641 Eh ::
:: repulsion energy 0.032111212067 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -5.070123981303 Eh |
| GRADIENT NORM 0.017792229436 Eh/α |
| HOMO-LUMO GAP 14.302156491823 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/04/28 at 11:27:34.626
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.039 sec
* cpu-time: 0 d, 0 h, 0 min, 0.007 sec
* ratio c/w: 0.169 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.033 sec
* cpu-time: 0 d, 0 h, 0 min, 0.001 sec
* ratio c/w: 0.041 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -5.070123981300
------------------------- --------------------
----------------------------------------------------------------------------
ORCA NUMERICAL FREQUENCIES
----------------------------------------------------------------------------
Number of atoms ... 3
Central differences ... used
Number of displacements ... 18
Numerical increment ... 5.000e-03 bohr
IR-spectrum generation ... on
Raman-spectrum generation ... off
Surface Crossing Hessian ... off
The output will be reduced. Please look at the following files:
SCF program output ... >cmmd.lastscf
Integral program output ... >cmmd.lastint
Gradient program output ... >cmmd.lastgrad
Dipole moment program output ... >cmmd.lastmom
AutoCI program output ... >cmmd.lastautoci
<< Calculating on displaced geometry 1 (of 18) >>
<< Calculating on displaced geometry 2 (of 18) >>
<< Calculating on displaced geometry 3 (of 18) >>
<< Calculating on displaced geometry 4 (of 18) >>
<< Calculating on displaced geometry 5 (of 18) >>
<< Calculating on displaced geometry 6 (of 18) >>
<< Calculating on displaced geometry 7 (of 18) >>
<< Calculating on displaced geometry 8 (of 18) >>
<< Calculating on displaced geometry 9 (of 18) >>
<< Calculating on displaced geometry 10 (of 18) >>
<< Calculating on displaced geometry 11 (of 18) >>
<< Calculating on displaced geometry 12 (of 18) >>
<< Calculating on displaced geometry 13 (of 18) >>
<< Calculating on displaced geometry 14 (of 18) >>
<< Calculating on displaced geometry 15 (of 18) >>
<< Calculating on displaced geometry 16 (of 18) >>
<< Calculating on displaced geometry 17 (of 18) >>
<< Calculating on displaced geometry 18 (of 18) >>
-----------------------
VIBRATIONAL FREQUENCIES
-----------------------
Scaling factor for frequencies = 1.000000000 (already applied!)
0: 0.00 cm**-1
1: 0.00 cm**-1
2: 0.00 cm**-1
3: 0.00 cm**-1
4: 0.00 cm**-1
5: 0.00 cm**-1
6: 1591.02 cm**-1
7: 3532.22 cm**-1
8: 3553.96 cm**-1
------------
NORMAL MODES
------------
These modes are the cartesian displacements weighted by the diagonal matrix
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
Thus, these vectors are normalized but *not* orthogonal
0 1 2 3 4 5
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
6 7 8
0 0.040721 -0.056762 -0.029045
1 0.045366 0.031729 -0.032147
2 0.035473 0.024811 -0.025137
3 0.027275 0.702670 0.707675
4 -0.555227 0.030998 -0.009740
5 -0.434156 0.024236 -0.007618
6 -0.673601 0.198259 -0.246669
7 -0.164818 -0.534607 0.519974
8 -0.128876 -0.418033 0.406591
-----------
IR SPECTRUM
-----------
Mode freq eps Int T**2 TX TY TZ
cm**-1 L/(mol*cm) km/mol a.u.
----------------------------------------------------------------------------
6: 1591.02 0.024022 121.40 0.004712 (-0.035425 -0.046627 -0.035815)
7: 3532.22 0.000687 3.47 0.000061 ( 0.006792 -0.003138 -0.002177)
8: 3553.96 0.002224 11.24 0.000195 ( 0.012984 0.004205 0.003002)
* The epsilon (eps) is given for a Dirac delta lineshape.
** The dipole moment derivative (T) already includes vibrational overlap.
The first frequency considered to be a vibration is 6
The total number of vibrations considered is 3
--------------------------
THERMOCHEMISTRY AT 298.15K
--------------------------
Temperature ... 298.15 K
Pressure ... 1.00 atm
Total Mass ... 18.02 AMU
Throughout the following assumptions are being made:
(1) The electronic state is orbitally nondegenerate
(2) There are no thermally accessible electronically excited states
(3) Hindered rotations indicated by low frequency modes are not
treated as such but are treated as vibrations and this may
cause some error
(4) All equations used are the standard statistical mechanics
equations for an ideal gas
(5) All vibrations are strictly harmonic
freq. 1591.02 E(vib) ... 0.00
freq. 3532.22 E(vib) ... 0.00
freq. 3553.96 E(vib) ... 0.00
------------
INNER ENERGY
------------
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans)
E(el) - is the total energy from the electronic structure calculation
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc)
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation
E(vib) - the the finite temperature correction to E(ZPE) due to population
of excited vibrational states
E(rot) - is the rotational thermal energy
E(trans)- is the translational thermal energy
Summary of contributions to the inner energy U:
Electronic energy ... -5.07012398 Eh
Zero point energy ... 0.01976814 Eh 12.40 kcal/mol
Thermal vibrational correction ... 0.00000336 Eh 0.00 kcal/mol
Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol
-----------------------------------------------------------------------
Total thermal energy -5.04751994 Eh
Summary of corrections to the electronic energy:
(perhaps to be used in another calculation)
Total thermal correction 0.00283590 Eh 1.78 kcal/mol
Non-thermal (ZPE) correction 0.01976814 Eh 12.40 kcal/mol
-----------------------------------------------------------------------
Total correction 0.02260404 Eh 14.18 kcal/mol
--------
ENTHALPY
--------
The enthalpy is H = U + kB*T
kB is Boltzmann's constant
Total free energy ... -5.04751994 Eh
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol
-----------------------------------------------------------------------
Total Enthalpy ... -5.04657573 Eh
Note: Rotational entropy computed according to Herzberg
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945
Point Group: C2v, Symmetry Number: 2
Rotational constants in cm-1: 26.033328 14.586495 9.348515
Vibrational entropy computed according to the QRRHO of S. Grimme
Chem.Eur.J. 2012 18 9955
-------
ENTROPY
-------
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans))
S(el) - electronic entropy
S(vib) - vibrational entropy
S(rot) - rotational entropy
S(trans)- translational entropy
The entropies will be listed as multiplied by the temperature to get
units of energy
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol
Vibrational entropy ... 0.00000380 Eh 0.00 kcal/mol
Rotational entropy ... 0.00499716 Eh 3.14 kcal/mol
Translational entropy ... 0.01644380 Eh 10.32 kcal/mol
-----------------------------------------------------------------------
Final entropy term ... 0.02144476 Eh 13.46 kcal/mol
In case the symmetry of your molecule has not been determined correctly
or in case you have a reason to use a different symmetry number we print
out the resulting rotational entropy values for sn=1,12 :
--------------------------------------------------------
| sn= 1 | S(rot)= 0.00565162 Eh 3.55 kcal/mol|
| sn= 2 | S(rot)= 0.00499716 Eh 3.14 kcal/mol|
| sn= 3 | S(rot)= 0.00461433 Eh 2.90 kcal/mol|
| sn= 4 | S(rot)= 0.00434270 Eh 2.73 kcal/mol|
| sn= 5 | S(rot)= 0.00413202 Eh 2.59 kcal/mol|
| sn= 6 | S(rot)= 0.00395987 Eh 2.48 kcal/mol|
| sn= 7 | S(rot)= 0.00381433 Eh 2.39 kcal/mol|
| sn= 8 | S(rot)= 0.00368825 Eh 2.31 kcal/mol|
| sn= 9 | S(rot)= 0.00357704 Eh 2.24 kcal/mol|
| sn=10 | S(rot)= 0.00347756 Eh 2.18 kcal/mol|
| sn=11 | S(rot)= 0.00338757 Eh 2.13 kcal/mol|
| sn=12 | S(rot)= 0.00330541 Eh 2.07 kcal/mol|
--------------------------------------------------------
-------------------
GIBBS FREE ENERGY
-------------------
The Gibbs free energy is G = H - T*S
Total enthalpy ... -5.04657573 Eh
Total entropy correction ... -0.02144476 Eh -13.46 kcal/mol
-----------------------------------------------------------------------
Final Gibbs free energy ... -5.06802049 Eh
For completeness - the Gibbs free energy minus the electronic energy
G-E(el) ... 0.00210349 Eh 1.32 kcal/mol
Timings for individual modules:
Sum of individual times ... 43.304 sec (= 0.722 min)
Numerical frequency calculation ... 43.071 sec (= 0.718 min) 99.5 %
XTB module ... 0.232 sec (= 0.004 min) 0.5 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 43 seconds 500 msec

@ -0,0 +1,5 @@
3
Coordinates from ORCA-job cmmd
O 0.92414308393591 0.05221745443381 -0.05277586891122
H 1.88956263013796 0.09467860003036 -0.01957714288512
H 0.65315428592613 0.78339394553583 0.51896301179633

@ -0,0 +1,42 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 18.0150000000
Spin Degeneracy : 1.0000000000
Electronic Energy (Hartree) : -5.0701239813
Translational Energy (Hartree) : 0.0014162714
Rotational Energy (Hartree) : 0.0014162714
Vibrational Energy (Hartree) : 0.0000033599
Number of frequencies : 9
Scaling Factor for frequencies : 1.0000000000
Vibrational frequencies :
0
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1591.021914
7 3532.222317
8 3553.964928
Zero Point Energy (Hartree) : 0.0197681370
Inner Energy (Hartree) : -5.0475199415
Enthalpy (Hartree) : -5.0465757325
Electronic entropy : 0.0000000000
Rotational entropy : 0.0049971600
Vibrational entropy : 0.0000037975
Translational entropy : 0.0049971600
Entropy : 0.0214447594
Gibbs Energy (Hartree) : -5.0680204919
Is Linear : false
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,25 @@
3
Coordinates from ORCA-job cmmd E -76.321237910070
O 0.925940 0.054220 -0.051210
H 1.893830 0.090800 -0.022610
H 0.647090 0.785270 0.520430
3
Coordinates from ORCA-job cmmd E -76.321265590472
O 0.925302 0.053508 -0.051766
H 1.890326 0.093285 -0.020667
H 0.651232 0.783496 0.519043
3
Coordinates from ORCA-job cmmd E -76.321269032868
O 0.924595 0.052721 -0.052382
H 1.889691 0.094230 -0.019928
H 0.652574 0.783339 0.518920
3
Coordinates from ORCA-job cmmd E -76.321269681211
O 0.924146 0.052221 -0.052773
H 1.889541 0.094688 -0.019570
H 0.653172 0.783381 0.518953
3
Coordinates from ORCA-job cmmd E -76.321269681391
O 0.924143 0.052217 -0.052776
H 1.889563 0.094679 -0.019577
H 0.653154 0.783394 0.518963

@ -0,0 +1,5 @@
3
O 0.92594 0.05422 -0.05121
H 1.89383 0.09080 -0.02261
H 0.64709 0.78527 0.52043

@ -0,0 +1,10 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

@ -0,0 +1,8 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel geom.smi -O geom.xyz --gen3d

@ -0,0 +1,22 @@
#
# Number of atoms
#
2
#
# The current total energy in Eh
#
-7.906649846780
#
# The current gradient in Eh/bohr
#
0.013068499674
-0.000000000007
-0.000000000001
-0.013068499674
0.000000000007
0.000000000001
#
# The atomic numbers and current coordinates in Bohr
#
8 1.9411149 -0.1746107 -0.0166863
8 4.2114933 -0.1746107 -0.0166863

Binary file not shown.

@ -0,0 +1,94 @@
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-7.906650
$hessian
6
0 1 2 3 4
0 8.4758564328E-01 -1.9586528653E-13 9.9420864020E-15 -8.4758564327E-01 4.4592567559E-13
1 -1.9586528653E-13 -5.7540195132E-03 -2.3384841278E-14 -9.0456931015E-13 5.7540195134E-03
2 9.9420864020E-15 -2.3384841278E-14 -5.7540195132E-03 -1.1572655252E-13 2.3972966388E-14
3 -8.4758564327E-01 -9.0456931015E-13 -1.1572655252E-13 8.4758564327E-01 6.5450892109E-13
4 4.4592567559E-13 5.7540195134E-03 2.3972966388E-14 6.5450892109E-13 -5.7540195136E-03
5 3.4003837488E-13 3.2581672750E-16 5.7540195134E-03 -2.3425390876E-13 -9.1394183800E-16
5
0 3.4003837488E-13
1 3.2581672750E-16
2 5.7540195134E-03
3 -2.3425390876E-13
4 -9.1394183800E-16
5 -5.7540195136E-03
$vibrational_frequencies
6
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 1673.234280
$normal_modes
6 6
0 1 2 3 4
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5
0 7.0710678119E-01
1 0.0000000000E+00
2 0.0000000000E+00
3 -7.0710678119E-01
4 0.0000000000E+00
5 0.0000000000E+00
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
2
O 15.99900 1.941114862176 -0.174610694774 -0.016686281763
O 15.99900 4.211493279168 -0.174610694774 -0.016686281763
$actual_temperature
0.000000
$frequency_scale_factor
1.000000
$dipole_derivatives
6
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
#
# The IR spectrum
# wavenumber eps Int TX TY TZ
#
$ir_spectrum
6
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
1673.23 0.00000000 0.00000000 0.000000 0.000000 0.000000
$end

@ -0,0 +1,13 @@
#CMMDE generated Orca input file
!XTB2 Numfreq
%pal
nprocs 1
end
*xyzfile 0 1 cmmd.xyz
%freq
scalfreq 1
Temp 298.15
Pressure 1.0
end

@ -0,0 +1,90 @@
$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
5 6
1.86498962 -0.17461069 -0.01668628 4.28761852 -0.17461069 -0.01668628
1.92904409 -0.17461069 -0.01668628 4.22356405 -0.17461069 -0.01668628
1.94530163 -0.17461069 -0.01668628 4.20730651 -0.17461069 -0.01668628
1.94090974 -0.17461069 -0.01668628 4.21169840 -0.17461069 -0.01668628
1.94110955 -0.17461069 -0.01668628 4.21149859 -0.17461069 -0.01668628
# redundant internal coordinates
# nbonds nangles ndihedrals nimpropers ncartesians
# bond definitions A B
# angle definitions A B C
# dihedral definitions A B C D
# improper torsion definitions A B C D
# cartesian definitions A x/y/z
$redundant_internals
1 0 0 0 0
1 0 0
$energies
5
-150.0735671197928411
-150.0814796331173113
-150.0816905296451864
-150.0817207523842285
-150.0817208238475189
$gradients
5 6
-0.0970701356891092 0.0000000037705223 -0.0000000020745829 0.0970701396000397
0.0000000041241647 0.0000000045418583
-0.0196664709248346 0.0000000000788218 -0.0000000002131847 0.0196664777184270
0.0000000059598546 0.0000000058290589
0.0072800276715361 0.0000000014684576 0.0000000012614792 -0.0072800235313076
-0.0000000014076424 0.0000000011235850
-0.0003470003285211 0.0000000013188094 0.0000000005114984 0.0003470040777374
-0.0000000019503669 -0.0000000003265739
-0.0000089794375978 0.0000000016304541 0.0000000005607051 0.0000089823666367
-0.0000000013571736 0.0000000007610567
$redundant_coords
5 1
2.4226289036870434
2.2945199680204644
2.2620048732196394
2.2707886655429821
2.2703890347982991
$redundant_gradients
5 1
0.0970701376445745
0.0196664743216308
-0.0072800256014219
0.0003470022031292
0.0000089809021172
$hessian_approx
6 6
0 1 2 3 4 5
0 0.845855 0.000001 0.000000 -0.845857 0.000001 0.000003
1 0.000001 0.000000 0.000000 -0.000001 0.000000 0.000000
2 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000
3 -0.845857 -0.000001 -0.000000 0.845859 -0.000001 -0.000003
4 0.000001 0.000000 0.000000 -0.000001 0.000000 0.000000
5 0.000003 0.000000 0.000000 -0.000003 0.000000 0.000000
$bmatrix
1 6
0 1 2 3 4 5
0 -1.000000 0.000000 0.000000 1.000000 -0.000000 -0.000000

@ -0,0 +1,612 @@
*****************
* O R C A *
*****************
#,
###
####
#####
######
########,
,,################,,,,,
,,#################################,,
,,##########################################,,
,#########################################, ''#####,
,#############################################,, '####,
,##################################################,,,,####,
,###########'''' ''''###############################
,#####'' ,,,,##########,,,, '''####''' '####
,##' ,,,,###########################,,, '##
' ,,###'''' '''############,,,
,,##'' '''############,,,, ,,,,,,###''
,#'' '''#######################'''
' ''''####''''
,#######, #######, ,#######, ##
,#' '#, ## ## ,#' '#, #''# ###### ,####,
## ## ## ,#' ## #' '# # #' '#
## ## ####### ## ,######, #####, # #
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,#
'#######' ## ## '#######' #' '# #####' # '####'
#######################################################
# -***- #
# Department of theory and spectroscopy #
# Directorship and core code : Frank Neese #
# Max Planck Institute fuer Kohlenforschung #
# Kaiser Wilhelm Platz 1 #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 5.0.2 - RELEASE -
With contributions from (in alphabetic order):
Daniel Aravena : Magnetic Suceptibility
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation)
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum
Ute Becker : Parallelization
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD
Martin Brehm : Molecular dynamics
Dmytro Bykov : SCF Hessian
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE
Dipayan Datta : RHF DLPNO-CCSD density
Achintya Kumar Dutta : EOM-CC, STEOM-CC
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
Lee Huntington : MR-EOM, pCC
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
Marcus Kettner : VPT2
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
Martin Krupicka : Initial AUTO-CI
Lucas Lang : DCDCAS
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC
Dagmar Lenk : GEPOL surface, SMD
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization
Dimitrios Manganas : Further ROCIS development; embedding schemes
Dimitrios Pantazis : SARC Basis sets
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient
Christoph Reimann : Effective Core Potentials
Marius Retegan : Local ZFS, SOC
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB
Michael Roemelt : Original ROCIS implementation
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density
Barbara Sandhoefer : DKH picture change effects
Avijit Sen : IP-ROCIS
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
Bernardo de Souza : ESD, SOC TD-DFT
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
Willem Van den Heuvel : Paramagnetic NMR
Boris Wezisla : Elementary symmetry handling
Frank Wennmohs : Technical directorship
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization,
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Jiri Pittner, Ondrej Demel : Mk-CCSD
Frank Weinhold : gennbo (NPA and NBO analysis)
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
Lars Goerigk : TD-DFT with DH, B97 family of functionals
V. Asgeirsson, H. Jonsson : NEB implementation
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
nearIR, NL-DFT gradient (VV10), updates on ESD,
ML-optimized integration grids
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library
Liviu Ungur et al : ANISO software
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
Your ORCA version has been built with support for libXC version: 5.1.0
For citations please refer to: https://tddft.org/programs/libxc/
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
SCALAPACK package : Parallel linear algebra routines
Shared memory : Shared parallel matrices
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
Core in use : SkylakeX
Copyright (c) 2011-2014, The OpenBLAS Project
***************************************
The coordinates will be read from file: cmmd.xyz
***************************************
Your calculation utilizes the semiempirical GFN2-xTB method
Please cite in your paper:
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652.
================================================================================
================================================================================
WARNINGS
Please study these warnings very carefully!
================================================================================
WARNING: Old DensityContainer found on disk!
Will remove this file -
If you want to keep old densities, please start your calculation with a different basename.
WARNING: Gradients needed for Numerical Frequencies
===> : Setting RunTyp to EnGrad
WARNING: Found dipole moment calculation with XTB calculation
===> : Switching off dipole moment calculation
WARNING: TRAH-SCF for XTB is not implemented!
===> : Turning TRAH off!
================================================================================
INPUT FILE
================================================================================
NAME = cmmd.in
| 1> #CMMDE generated Orca input file
| 2> !XTB2 Numfreq
| 3> %pal
| 4> nprocs 1
| 5> end
| 6>
| 7> *xyzfile 0 1 cmmd.xyz
| 8>
| 9> %freq
| 10> scalfreq 1
| 11> Temp 298.15
| 12> Pressure 1.0
| 13> end
| 14>
| 15> ****END OF INPUT****
================================================================================
*******************************
* Energy+Gradient Calculation *
*******************************
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/04/28 at 11:27:40.328
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 2
number of electrons : 12
charge : 0
spin : 0.0
first test random number : 0.84096853316258
ID Z sym. atoms
1 8 O 1, 2
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
...................................................
: SETUP :
:.................................................:
: # basis functions 8 :
: # atomic orbitals 8 :
: # shells 4 :
: # electrons 12 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -7.9155572 -0.791556E+01 0.407E+00 0.00 0.0 T
2 -7.9155697 -0.125362E-04 0.246E+00 0.00 1.0 T
3 -7.9155792 -0.944533E-05 0.542E-02 0.00 1.3 T
4 -7.9155792 -0.302522E-08 0.166E-02 0.00 4.3 T
5 -7.9155792 -0.836504E-10 0.345E-05 0.00 2049.3 T
6 -7.9155792 0.355271E-14 0.271E-07 0.00 100000.0 T
*** convergence criteria satisfied after 6 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.8284027 -22.5420
2 2.0000 -0.7371506 -20.0589
3 2.0000 -0.6631440 -18.0451
4 2.0000 -0.6631440 -18.0451
5 2.0000 -0.6374674 -17.3464
6 1.0000 -0.4399644 -11.9720 (HOMO)
7 1.0000 -0.4399644 -11.9720 (LUMO)
8 0.1444079 3.9295
-------------------------------------------------------------
HL-Gap 0.0000000 Eh 0.0000 eV
Fermi-level -0.4399644 Eh -11.9720 eV
SCC (total) 0 d, 0 h, 0 min, 0.050 sec
SCC setup ... 0 min, 0.000 sec ( 0.151%)
Dispersion ... 0 min, 0.000 sec ( 0.040%)
classical contributions ... 0 min, 0.000 sec ( 0.017%)
integral evaluation ... 0 min, 0.000 sec ( 0.294%)
iterations ... 0 min, 0.050 sec ( 98.980%)
molecular gradient ... 0 min, 0.000 sec ( 0.333%)
printout ... 0 min, 0.000 sec ( 0.168%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -7.906649846778 Eh ::
:: gradient norm 0.018481649479 Eh/a0 ::
:: HOMO-LUMO gap 0.000000000015 eV ::
::.................................................::
:: SCC energy -7.915579172539 Eh ::
:: -> isotropic ES -0.000237652172 Eh ::
:: -> anisotropic ES 0.003738001563 Eh ::
:: -> anisotropic XC -0.007283115557 Eh ::
:: -> dispersion -0.000194539012 Eh ::
:: repulsion energy 0.008929325760 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -7.906649846778 Eh |
| GRADIENT NORM 0.018481649479 Eh/α |
| HOMO-LUMO GAP 0.000000000015 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/04/28 at 11:27:40.387
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.059 sec
* cpu-time: 0 d, 0 h, 0 min, 0.012 sec
* ratio c/w: 0.196 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.050 sec
* cpu-time: 0 d, 0 h, 0 min, 0.003 sec
* ratio c/w: 0.058 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -7.906649846780
------------------------- --------------------
----------------------------------------------------------------------------
ORCA NUMERICAL FREQUENCIES
----------------------------------------------------------------------------
Number of atoms ... 2
Central differences ... used
Number of displacements ... 12
Numerical increment ... 5.000e-03 bohr
IR-spectrum generation ... on
Raman-spectrum generation ... off
Surface Crossing Hessian ... off
The output will be reduced. Please look at the following files:
SCF program output ... >cmmd.lastscf
Integral program output ... >cmmd.lastint
Gradient program output ... >cmmd.lastgrad
Dipole moment program output ... >cmmd.lastmom
AutoCI program output ... >cmmd.lastautoci
<< Calculating on displaced geometry 1 (of 12) >>
<< Calculating on displaced geometry 2 (of 12) >>
<< Calculating on displaced geometry 3 (of 12) >>
<< Calculating on displaced geometry 4 (of 12) >>
<< Calculating on displaced geometry 5 (of 12) >>
<< Calculating on displaced geometry 6 (of 12) >>
<< Calculating on displaced geometry 7 (of 12) >>
<< Calculating on displaced geometry 8 (of 12) >>
<< Calculating on displaced geometry 9 (of 12) >>
<< Calculating on displaced geometry 10 (of 12) >>
<< Calculating on displaced geometry 11 (of 12) >>
<< Calculating on displaced geometry 12 (of 12) >>
-----------------------
VIBRATIONAL FREQUENCIES
-----------------------
Scaling factor for frequencies = 1.000000000 (already applied!)
0: 0.00 cm**-1
1: 0.00 cm**-1
2: 0.00 cm**-1
3: 0.00 cm**-1
4: 0.00 cm**-1
5: 1673.23 cm**-1
------------
NORMAL MODES
------------
These modes are the cartesian displacements weighted by the diagonal matrix
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
Thus, these vectors are normalized but *not* orthogonal
0 1 2 3 4 5
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.707107
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3 0.000000 0.000000 0.000000 0.000000 0.000000 -0.707107
4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-----------
IR SPECTRUM
-----------
Mode freq eps Int T**2 TX TY TZ
cm**-1 L/(mol*cm) km/mol a.u.
----------------------------------------------------------------------------
5: 1673.23 0.000000 0.00 0.000000 ( 0.000000 0.000000 0.000000)
* The epsilon (eps) is given for a Dirac delta lineshape.
** The dipole moment derivative (T) already includes vibrational overlap.
The first frequency considered to be a vibration is 5
The total number of vibrations considered is 1
--------------------------
THERMOCHEMISTRY AT 298.15K
--------------------------
Temperature ... 298.15 K
Pressure ... 1.00 atm
Total Mass ... 32.00 AMU
The molecule is recognized as being linear
Throughout the following assumptions are being made:
(1) The electronic state is orbitally nondegenerate
(2) There are no thermally accessible electronically excited states
(3) Hindered rotations indicated by low frequency modes are not
treated as such but are treated as vibrations and this may
cause some error
(4) All equations used are the standard statistical mechanics
equations for an ideal gas
(5) All vibrations are strictly harmonic
freq. 1673.23 E(vib) ... 0.00
------------
INNER ENERGY
------------
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans)
E(el) - is the total energy from the electronic structure calculation
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc)
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation
E(vib) - the the finite temperature correction to E(ZPE) due to population
of excited vibrational states
E(rot) - is the rotational thermal energy
E(trans)- is the translational thermal energy
Summary of contributions to the inner energy U:
Electronic energy ... -7.90664985 Eh
Zero point energy ... 0.00381191 Eh 2.39 kcal/mol
Thermal vibrational correction ... 0.00000238 Eh 0.00 kcal/mol
Thermal rotational correction ... 0.00094418 Eh 0.59 kcal/mol
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol
-----------------------------------------------------------------------
Total thermal energy -7.90047511 Eh
Summary of corrections to the electronic energy:
(perhaps to be used in another calculation)
Total thermal correction 0.00236283 Eh 1.48 kcal/mol
Non-thermal (ZPE) correction 0.00381191 Eh 2.39 kcal/mol
-----------------------------------------------------------------------
Total correction 0.00617474 Eh 3.87 kcal/mol
--------
ENTHALPY
--------
The enthalpy is H = U + kB*T
kB is Boltzmann's constant
Total free energy ... -7.90047511 Eh
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol
-----------------------------------------------------------------------
Total Enthalpy ... -7.89953090 Eh
Note: Rotational entropy computed according to Herzberg
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945
Point Group: Dinfh, Symmetry Number: 2
Rotational constants in cm-1: 0.000000 1.459941 1.459941
Vibrational entropy computed according to the QRRHO of S. Grimme
Chem.Eur.J. 2012 18 9955
-------
ENTROPY
-------
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans))
S(el) - electronic entropy
S(vib) - vibrational entropy
S(rot) - rotational entropy
S(trans)- translational entropy
The entropies will be listed as multiplied by the temperature to get
units of energy
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol
Vibrational entropy ... 0.00000267 Eh 0.00 kcal/mol
Rotational entropy ... 0.00496853 Eh 3.12 kcal/mol
Translational entropy ... 0.01725741 Eh 10.83 kcal/mol
-----------------------------------------------------------------------
Final entropy term ... 0.02222861 Eh 13.95 kcal/mol
-------------------
GIBBS FREE ENERGY
-------------------
The Gibbs free energy is G = H - T*S
Total enthalpy ... -7.89953090 Eh
Total entropy correction ... -0.02222861 Eh -13.95 kcal/mol
-----------------------------------------------------------------------
Final Gibbs free energy ... -7.92175951 Eh
For completeness - the Gibbs free energy minus the electronic energy
G-E(el) ... -0.01510966 Eh -9.48 kcal/mol
Timings for individual modules:
Sum of individual times ... 30.549 sec (= 0.509 min)
Numerical frequency calculation ... 30.380 sec (= 0.506 min) 99.4 %
XTB module ... 0.169 sec (= 0.003 min) 0.6 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 30 seconds 827 msec

@ -0,0 +1,4 @@
2
Coordinates from ORCA-job cmmd
O 1.02719374375572 -0.09240000000000 -0.00883000000000
O 2.22862625624428 -0.09240000000000 -0.00883000000000

@ -0,0 +1,39 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 31.9980000000
Spin Degeneracy : 1.0000000000
Electronic Energy (Hartree) : -7.9066498468
Translational Energy (Hartree) : 0.0014162714
Rotational Energy (Hartree) : 0.0009441809
Vibrational Energy (Hartree) : 0.0000023751
Number of frequencies : 6
Scaling Factor for frequencies : 1.0000000000
Vibrational frequencies :
0
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 1673.234280
Zero Point Energy (Hartree) : 0.0038119082
Inner Energy (Hartree) : -7.9004751111
Enthalpy (Hartree) : -7.8995309021
Electronic entropy : 0.0000000000
Rotational entropy : 0.0049685321
Vibrational entropy : 0.0000026695
Translational entropy : 0.0049685321
Entropy : 0.0222286070
Gibbs Energy (Hartree) : -7.9217595090
Is Linear : false
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,24 @@
2
Coordinates from ORCA-job cmmd E -150.073567119793
O 0.986910 -0.092400 -0.008830
O 2.268910 -0.092400 -0.008830
2
Coordinates from ORCA-job cmmd E -150.081479633117
O 1.020806 -0.092400 -0.008830
O 2.235014 -0.092400 -0.008830
2
Coordinates from ORCA-job cmmd E -150.081690529645
O 1.029409 -0.092400 -0.008830
O 2.226411 -0.092400 -0.008830
2
Coordinates from ORCA-job cmmd E -150.081720752384
O 1.027085 -0.092400 -0.008830
O 2.228735 -0.092400 -0.008830
2
Coordinates from ORCA-job cmmd E -150.081720823848
O 1.027191 -0.092400 -0.008830
O 2.228629 -0.092400 -0.008830
2
Coordinates from ORCA-job cmmd E -150.081720823916
O 1.027194 -0.092400 -0.008830
O 2.228626 -0.092400 -0.008830

@ -0,0 +1,4 @@
2
O 0.98691 -0.09240 -0.00883
O 2.26891 -0.09240 -0.00883

@ -0,0 +1,10 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

@ -0,0 +1,8 @@
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel geom.smi -O geom.xyz --gen3d

@ -0,0 +1,21 @@
[ (resname_SLV) ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270
271 272 273 274 275 276 277 278 279 280 281 282 283 284 285
286 287 288 289 290 291 292 293 294 295 296 297 298 299 300

@ -0,0 +1,8 @@
[ (resname_URA) ]
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315
316 317 318 319 320 321 322 323 324 325 326 327 328 329 330
331 332 333 334 335 336 337 338 339 340 341 342 343 344 345
346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375
376 377 378 379 380 381 382 383 384 385 386 387 388 389 390
391 392 393 394 395 396 397 398 399 400 401 402 403 404

@ -0,0 +1,5 @@
; to test
; gmx grompp -f em.mdp -c system_GMX.gro -p system_GMX.top -o em.tpr -v
; gmx mdrun -ntmpi 1 -v -deffnm em
integrator = steep
nsteps = 500

File diff suppressed because it is too large Load Diff

@ -0,0 +1,297 @@
log started: Thu Apr 28 23:05:06 2022
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> # This file is mostly for use with Antechamber
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "h1" "H" "sp3" }
>> { "h2" "H" "sp3" }
>> { "h3" "H" "sp3" }
>> { "h4" "H" "sp3" }
>> { "h5" "H" "sp3" }
>> { "ha" "H" "sp3" }
>> { "hc" "H" "sp3" }
>> { "hn" "H" "sp3" }
>> { "ho" "H" "sp3" }
>> { "hp" "H" "sp3" }
>> { "hs" "H" "sp3" }
>> { "hw" "H" "sp3" }
>> { "hx" "H" "sp3" }
>> { "o" "O" "sp2" }
>> { "o2" "O" "sp2" }
>> { "oh" "O" "sp3" }
>> { "op" "O" "sp3" }
>> { "oq" "O" "sp3" }
>> { "os" "O" "sp3" }
>> { "ow" "O" "sp3" }
>> { "c" "C" "sp2" }
>> { "c1" "C" "sp2" }
>> { "c2" "C" "sp2" }
>> { "c3" "C" "sp3" }
>> { "ca" "C" "sp2" }
>> { "cc" "C" "sp2" }
>> { "cd" "C" "sp2" }
>> { "ce" "C" "sp2" }
>> { "cf" "C" "sp2" }
>> { "cg" "C" "sp2" }
>> { "ch" "C" "sp2" }
>> { "cp" "C" "sp2" }
>> { "cq" "C" "sp2" }
>> { "cu" "C" "sp2" }
>> { "cv" "C" "sp2" }
>> { "cx" "C" "sp2" }
>> { "cy" "C" "sp2" }
>> { "cz" "C" "sp2" }
>> { "n" "N" "sp2" }
>> { "n1" "N" "sp2" }
>> { "n2" "N" "sp2" }
>> { "n3" "N" "sp3" }
>> { "n4" "N" "sp3" }
>> { "na" "N" "sp2" }
>> { "nb" "N" "sp2" }
>> { "nc" "N" "sp2" }
>> { "nd" "N" "sp2" }
>> { "ne" "N" "sp2" }
>> { "nf" "N" "sp2" }
>> { "nh" "N" "sp2" }
>> { "ni" "N" "sp2" }
>> { "nj" "N" "sp2" }
>> { "nk" "N" "sp3" }
>> { "nl" "N" "sp3" }
>> { "nm" "N" "sp2" }
>> { "nn" "N" "sp2" }
>> { "no" "N" "sp2" }
>> { "np" "N" "sp3" }
>> { "nq" "N" "sp3" }
>> { "s" "S" "sp2" }
>> { "s2" "S" "sp2" }
>> { "s3" "S" "sp3" }
>> { "s4" "S" "sp3" }
>> { "s6" "S" "sp3" }
>> { "sh" "S" "sp3" }
>> { "sp" "S" "sp3" }
>> { "sq" "S" "sp3" }
>> { "ss" "S" "sp3" }
>> { "sx" "S" "sp3" }
>> { "sy" "S" "sp3" }
>> { "p2" "P" "sp2" }
>> { "p3" "P" "sp3" }
>> { "p4" "P" "sp3" }
>> { "p5" "P" "sp3" }
>> { "pb" "P" "sp3" }
>> { "pc" "P" "sp3" }
>> { "pd" "P" "sp3" }
>> { "pe" "P" "sp3" }
>> { "pf" "P" "sp3" }
>> { "px" "P" "sp3" }
>> { "py" "P" "sp3" }
>> { "f" "F" "sp3" }
>> { "cl" "Cl" "sp3" }
>> { "br" "Br" "sp3" }
>> { "i" "I" "sp3" }
>> }
>> #
>> # Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /home/adit/miniconda3/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
>
> loadamberparams /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod
Loading parameters: /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P, SPC/E and TIP4P/EW water models (12-6 IOD set)
(UNKNOWN ATOM TYPE: Li+)
(UNKNOWN ATOM TYPE: Na+)
(UNKNOWN ATOM TYPE: K+)
(UNKNOWN ATOM TYPE: Rb+)
(UNKNOWN ATOM TYPE: Cs+)
(UNKNOWN ATOM TYPE: Tl+)
(UNKNOWN ATOM TYPE: Cu+)
(UNKNOWN ATOM TYPE: Ag+)
(UNKNOWN ATOM TYPE: NH4+)
(UNKNOWN ATOM TYPE: HE+)
(UNKNOWN ATOM TYPE: HZ+)
(UNKNOWN ATOM TYPE: H3O+)
(UNKNOWN ATOM TYPE: F-)
(UNKNOWN ATOM TYPE: Cl-)
(UNKNOWN ATOM TYPE: Br-)
(UNKNOWN ATOM TYPE: I-)
> loadoff ../urea/URA.lib
Loading library: ../urea/URA.lib
Loading: URA
> loadamberparams ../urea/urea.frcmod
Loading parameters: ../urea/urea.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadoff ../water/water.lib
Loading library: ../water/water.lib
Loading: SLV
> loadamberparams ../water/water.frcmod
Loading parameters: ../water/water.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> SYSTEM = loadpdb system_init.pdb
Loading PDB file: ./system_init.pdb
(starting new molecule for chain B)
Matching PDB residue names to LEaP variables.
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
total atoms in file: 404
> list
SLV SYSTEM URA gaff
> saveamberparm SYSTEM system.prmtop system.inpcrd
Checking Unit.
/home/adit/miniconda3/bin/teLeap: Warning!
The unperturbed charge of the unit (-0.013100) is not integral.
/home/adit/miniconda3/bin/teLeap: Warning!
The unperturbed charge of the unit (-0.013100) is not zero.
/home/adit/miniconda3/bin/teLeap: Note.
Ignoring the error and warning from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 39 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
SLV 100
URA 13
)
(no restraints)
> savepdb SYSTEM system.pdb
Writing pdb file: system.pdb
> quit
Quit
Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1.

@ -0,0 +1,5 @@
; to test
; gmx grompp -f md.mdp -c em.gro -p system_GMX.top -o md.tpr
; gmx mdrun -ntmpi 1 -v -deffnm md
integrator = md
nsteps = 10000

@ -0,0 +1,312 @@
;
; File 'mdout.mdp' was generated
; By user: unknown (1000)
; On host: compute
; At date: Thu Apr 28 23:06:12 2022
;
; Created by:
; :-) GROMACS - gmx grompp, 2021.3 (-:
;
; Executable: /usr/local/gromacs/bin/gmx
; Data prefix: /usr/local/gromacs
; Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
; Command line:
; gmx -quiet grompp -c npt.gro -f nvep.mdp -maxwarn 2 -o nvep.tpr -p system_GMX.top
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.0005
nsteps = 10000
; For exact run continuation or redoing part of a run
init-step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part = 1
; Multiple time-stepping
mts = no
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 100
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = -1
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax-shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 500
nstvout = 500
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 500
nstcalcenergy = 100
nstenergy = 500
; Output frequency and precision for .xtc file
nstxout-compressed = 0
compressed-x-precision = 1000
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs)
cutoff-scheme = Verlet
; nblist update frequency
nstlist = 10
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
; nblist cut-off
rlist = 1
; long-range cut-off for switched potentials
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 0.7113990804113833
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon-rf = 0
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch = 0
rvdw = 0.7113990804113833
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Separate tables between energy group pairs
energygrp-table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.16
; FFT grid size, when a value is 0 fourierspacing will be used
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = no
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps =
; Time constant (ps) and reference temperature (K)
tau-t =
ref-t =
; pressure coupling
pcoupl = no
pcoupltype = Isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility =
ref-p =
; Scaling of reference coordinates, No, All or COM
refcoord-scaling = No
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated with MiMiC
QMMM-grps =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing-npoints =
; List of times at the annealing points for each group
annealing-time =
; Temp. at each annealing point, for each group.
annealing-temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen-temp = 300
gen-seed = -1
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp-excl =
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype =
wall-density =
wall-ewald-zfac = 3
; COM PULLING
pull = no
; AWH biasing
awh = no
; ENFORCED ROTATION
; Enforced rotation: No or Yes
rotation = no
; Group to display and/or manipulate in interactive MD session
IMD-group =
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Free energy variables
free-energy = no
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
init-lambda = -1
init-lambda-state = -1
delta-lambda = 0
nstdhdl = 50
fep-lambdas =
mass-lambdas =
coul-lambdas =
vdw-lambdas =
bonded-lambdas =
restraint-lambdas =
temperature-lambdas =
calc-lambda-neighbors = 1
init-lambda-weights =
dhdl-print-energy = no
sc-alpha = 0
sc-power = 1
sc-r-power = 6
sc-sigma = 0.3
sc-coul = no
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; simulated tempering variables
simulated-tempering = no
simulated-tempering-scaling = geometric
sim-temp-low = 300
sim-temp-high = 300
; Ion/water position swapping for computational electrophysiology setups
; Swap positions along direction: no, X, Y, Z
swapcoords = no
adress = no
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
; Electric fields
; Format for electric-field-x, etc. is: four real variables:
; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
; and sigma (ps) width of the pulse. Omega = 0 means static field,
; sigma = 0 means no pulse, leaving the field to be a cosine function.
electric-field-x = 0 0 0 0
electric-field-y = 0 0 0 0
electric-field-z = 0 0 0 0
; Density guided simulation
density-guided-simulation-active = false

@ -0,0 +1,407 @@
system
404
1SLV O 1 0.682 0.076 0.216
1SLV H 2 0.707 0.147 0.279
1SLV H1 3 0.583 0.083 0.210
2SLV O 4 0.361 0.189 0.582
2SLV H 5 0.384 0.273 0.535
2SLV H1 6 0.432 0.180 0.650
3SLV O 7 0.020 0.744 1.097
3SLV H 8 0.038 0.749 0.999
3SLV H1 9 0.112 0.742 1.135
4SLV O 10 0.355 1.129 0.948
4SLV H 11 0.295 1.162 0.876
4SLV H1 12 0.379 1.038 0.916
5SLV O 13 0.087 1.162 0.060
5SLV H 14 0.098 1.104 1.603
5SLV H1 15 0.036 1.106 0.124
6SLV O 16 0.134 0.823 0.010
6SLV H 17 0.040 0.802 1.609
6SLV H1 18 0.154 0.893 1.565
7SLV O 19 0.079 0.809 0.826
7SLV H 20 0.176 0.818 0.813
7SLV H1 21 0.045 0.785 0.737
8SLV O 22 1.173 0.813 0.137
8SLV H 23 1.126 0.852 0.214
8SLV H1 24 1.225 0.887 0.101
9SLV O 25 0.563 1.519 1.520
9SLV H 26 0.652 1.564 1.534
9SLV H1 27 0.530 1.502 1.611
10SLV O 28 1.336 1.262 1.030
10SLV H 29 1.434 1.253 1.032
10SLV H1 30 1.317 1.314 0.949
11SLV O 31 1.019 1.340 0.333
11SLV H 32 1.040 1.281 0.257
11SLV H1 33 1.063 1.292 0.408
12SLV O 34 0.193 1.213 0.738
12SLV H 35 0.143 1.295 0.713
12SLV H1 36 0.118 1.153 0.764
13SLV O 37 0.752 1.306 0.021
13SLV H 38 0.733 1.316 1.548
13SLV H1 39 0.679 1.248 0.054
14SLV O 40 1.175 0.828 0.973
14SLV H 41 1.114 0.798 1.046
14SLV H1 42 1.183 0.748 0.917
15SLV O 43 1.469 0.539 0.098
15SLV H 44 1.409 0.511 0.171
15SLV H1 45 1.554 0.494 0.122
16SLV O 46 1.152 0.062 0.652
16SLV H 47 1.168 1.610 0.716
16SLV H1 48 1.070 0.104 0.687
17SLV O 49 0.465 0.804 1.547
17SLV H 50 0.563 0.818 1.554
17SLV H1 51 0.430 0.831 0.012
18SLV O 52 0.169 0.223 1.492
18SLV H 53 0.231 0.260 1.559
18SLV H1 54 0.143 0.134 1.528
19SLV O 55 0.757 1.249 0.391
19SLV H 56 0.701 1.332 0.397
19SLV H1 57 0.846 1.286 0.368
20SLV O 58 0.411 0.068 0.238
20SLV H 59 0.323 0.097 0.271
20SLV H1 60 0.388 1.607 0.189
21SLV O 61 0.366 0.854 0.179
21SLV H 62 0.272 0.852 0.145
21SLV H1 63 0.356 0.883 0.273
22SLV O 64 1.061 1.354 1.597
22SLV H 65 1.033 1.269 0.019
22SLV H1 66 0.977 1.406 1.601
23SLV O 67 0.081 0.406 0.163
23SLV H 68 0.129 0.460 0.095
23SLV H1 69 0.120 0.317 0.149
24SLV O 70 0.352 0.532 1.025
24SLV H 71 0.296 0.451 1.026
24SLV H1 72 0.428 0.510 1.086
25SLV O 73 0.549 0.964 1.188
25SLV H 74 0.511 1.054 1.193
25SLV H1 75 0.645 0.979 1.186
26SLV O 76 0.099 0.038 0.657
26SLV H 77 0.069 1.566 0.660
26SLV H1 78 0.193 0.032 0.684
27SLV O 79 0.007 1.274 1.375
27SLV H 80 0.099 1.307 1.396
27SLV H1 81 1.576 1.313 1.447
28SLV O 82 1.605 1.078 0.850
28SLV H 83 0.001 0.982 0.859
28SLV H1 84 1.609 1.116 0.941
29SLV O 85 0.636 1.173 0.838
29SLV H 86 0.550 1.172 0.792
29SLV H1 87 0.613 1.156 0.932
30SLV O 88 0.562 1.084 0.064
30SLV H 89 0.624 1.007 0.065
30SLV H1 90 0.502 1.070 0.141
31SLV O 91 1.134 0.145 1.269
31SLV H 92 1.082 0.060 1.268
31SLV H1 93 1.132 0.167 1.366
32SLV O 94 0.693 1.345 1.342
32SLV H 95 0.634 1.409 1.390
32SLV H1 96 0.632 1.303 1.276
33SLV O 97 0.427 0.546 1.453
33SLV H 98 0.444 0.642 1.475
33SLV H1 99 0.337 0.533 1.493
34SLV O 100 1.448 0.232 0.875
34SLV H 101 1.477 0.239 0.970
34SLV H1 102 1.535 0.251 0.829
35SLV O 103 1.582 1.621 0.335
35SLV H 104 1.526 0.045 0.402
35SLV H1 105 0.047 0.043 0.345
36SLV O 106 0.086 1.584 1.544
36SLV H 107 0.046 1.588 1.454
36SLV H1 108 0.025 1.520 1.590
37SLV O 109 1.341 0.336 1.573
37SLV H 110 1.390 0.257 1.607
37SLV H1 111 1.391 0.413 1.609
38SLV O 112 1.316 1.190 0.002
38SLV H 113 1.329 1.140 1.539
38SLV H1 114 1.232 1.240 1.607
39SLV O 115 1.065 1.058 0.813
39SLV H 116 0.974 1.053 0.850
39SLV H1 117 1.112 0.993 0.871
40SLV O 118 0.347 1.457 0.099
40SLV H 119 0.338 1.377 0.157
40SLV H1 120 0.257 1.472 0.064
41SLV O 121 0.568 0.106 0.755
41SLV H 122 0.655 0.063 0.767
41SLV H1 123 0.502 0.038 0.785
42SLV O 124 0.094 1.018 1.443
42SLV H 125 0.048 0.962 1.376
42SLV H1 126 0.071 1.108 1.411
43SLV O 127 1.186 1.559 0.396
43SLV H 128 1.122 1.486 0.376
43SLV H1 129 1.157 1.591 0.486
44SLV O 130 0.185 0.109 1.228
44SLV H 131 0.114 0.045 1.251
44SLV H1 132 0.212 0.147 1.315
45SLV O 133 0.003 1.218 1.101
45SLV H 134 0.082 1.276 1.086
45SLV H1 135 1.610 1.235 1.198
46SLV O 136 1.133 1.470 0.837
46SLV H 137 1.064 1.411 0.798
46SLV H1 138 1.083 1.528 0.900
47SLV O 139 0.178 0.177 0.365
47SLV H 140 0.223 0.171 0.454
47SLV H1 141 0.161 0.273 0.356
48SLV O 142 0.920 1.572 0.139
48SLV H 143 0.930 1.495 0.199
48SLV H1 144 0.834 1.613 0.168
49SLV O 145 0.462 0.101 1.367
49SLV H 146 0.493 0.026 1.424
49SLV H1 147 0.496 0.181 1.414
50SLV O 148 0.815 0.017 1.511
50SLV H 149 0.867 0.002 1.594
50SLV H1 150 0.882 0.010 1.439
51SLV O 151 1.138 0.639 1.436
51SLV H 152 1.221 0.656 1.386
51SLV H1 153 1.168 0.596 1.518
52SLV O 154 0.751 0.619 0.456
52SLV H 155 0.716 0.635 0.366
52SLV H1 156 0.784 0.526 0.451
53SLV O 157 0.450 0.560 0.165
53SLV H 158 0.544 0.558 0.132
53SLV H1 159 0.423 0.654 0.155
54SLV O 160 1.261 1.512 0.090
54SLV H 161 1.217 1.526 0.177
54SLV H1 162 1.193 1.464 0.037
55SLV O 163 1.361 0.703 1.273
55SLV H 164 1.303 0.753 1.211
55SLV H1 165 1.444 0.690 1.221
56SLV O 166 1.006 1.131 0.121
56SLV H 167 0.919 1.095 0.096
56SLV H1 168 1.035 1.075 0.198
57SLV O 169 1.434 0.109 0.114
57SLV H 170 1.375 0.034 0.088
57SLV H1 171 1.501 0.062 0.170
58SLV O 172 0.280 1.229 0.244
58SLV H 173 0.210 1.204 0.178
58SLV H1 174 0.248 1.192 0.329
59SLV O 175 1.456 1.358 0.439
59SLV H 176 1.401 1.437 0.423
59SLV H1 177 1.540 1.379 0.393
60SLV O 178 0.420 1.105 1.450
60SLV H 179 0.409 1.011 1.425
60SLV H1 180 0.468 1.101 1.537
61SLV O 181 0.337 1.575 0.820
61SLV H 182 0.315 1.500 0.879
61SLV H1 183 0.308 0.032 0.874
62SLV O 184 0.377 1.537 0.530
62SLV H 185 0.365 0.012 0.530
62SLV H1 186 0.364 1.513 0.625
63SLV O 187 1.014 0.045 0.997
63SLV H 188 0.969 0.111 0.939
63SLV H1 189 1.075 0.099 1.052
64SLV O 190 0.567 0.317 1.514
64SLV H 191 0.524 0.402 1.487
64SLV H1 192 0.662 0.341 1.518
65SLV O 193 1.337 1.053 1.383
65SLV H 194 1.273 1.066 1.311
65SLV H1 195 1.418 1.019 1.335
66SLV O 196 0.176 0.556 1.571
66SLV H 197 0.115 0.544 1.495
66SLV H1 198 0.169 0.654 1.592
67SLV O 199 1.375 0.123 0.483
67SLV H 200 1.319 0.131 0.565
67SLV H1 201 1.319 0.061 0.429
68SLV O 202 0.289 0.765 1.174
68SLV H 203 0.369 0.822 1.188
68SLV H1 204 0.322 0.689 1.120
69SLV O 205 1.274 1.189 0.288
69SLV H 206 1.300 1.192 0.193
69SLV H1 207 1.350 1.228 0.338
70SLV O 208 0.975 0.407 1.224
70SLV H 209 0.951 0.422 1.131
70SLV H1 210 1.003 0.313 1.229
71SLV O 211 0.550 0.490 1.214
71SLV H 212 0.639 0.506 1.255
71SLV H1 213 0.491 0.508 1.292
72SLV O 214 0.614 1.483 0.396
72SLV H 215 0.523 1.500 0.433
72SLV H1 216 0.625 1.549 0.325
73SLV O 217 1.326 0.339 1.197
73SLV H 218 1.279 0.419 1.229
73SLV H1 219 1.264 0.265 1.221
74SLV O 220 0.505 1.263 1.139
74SLV H 221 0.439 1.221 1.078
74SLV H1 222 0.476 1.358 1.141
75SLV O 223 1.393 0.459 0.718
75SLV H 224 1.487 0.482 0.701
75SLV H1 225 1.400 0.377 0.774
76SLV O 226 1.104 0.330 0.237
76SLV H 227 1.199 0.335 0.262
76SLV H1 228 1.055 0.368 0.313
77SLV O 229 0.931 1.573 1.256
77SLV H 230 0.866 1.500 1.272
77SLV H1 231 0.925 1.590 1.159
78SLV O 232 0.457 0.907 0.811
78SLV H 233 0.552 0.932 0.813
78SLV H1 234 0.460 0.816 0.771
79SLV O 235 1.579 0.257 1.114
79SLV H 236 1.502 0.297 1.163
79SLV H1 237 0.011 0.212 1.182
80SLV O 238 1.121 1.241 0.589
80SLV H 239 1.101 1.176 0.662
80SLV H1 240 1.218 1.251 0.592
81SLV O 241 0.685 0.436 0.741
81SLV H 242 0.656 0.391 0.823
81SLV H1 243 0.729 0.364 0.691
82SLV O 244 0.483 0.649 0.709
82SLV H 245 0.560 0.600 0.669
82SLV H1 246 0.425 0.576 0.739
83SLV O 247 1.380 0.327 0.289
83SLV H 248 1.403 0.261 0.217
83SLV H1 249 1.390 0.271 0.370
84SLV O 250 1.613 1.398 0.685
84SLV H 251 1.544 1.455 0.728
84SLV H1 252 1.560 1.348 0.619
85SLV O 253 0.272 1.336 1.422
85SLV H 254 0.325 1.251 1.428
85SLV H1 255 0.322 1.396 1.482
86SLV O 256 1.440 1.601 0.752
86SLV H 257 1.416 0.049 0.816
86SLV H1 258 1.484 0.028 0.680
87SLV O 259 0.205 1.414 1.161
87SLV H 260 0.226 1.382 1.253
87SLV H1 261 0.277 1.480 1.146
88SLV O 262 1.570 1.589 1.266
88SLV H 263 1.477 1.614 1.249
88SLV H1 264 1.586 1.512 1.207
89SLV O 265 0.456 0.350 0.360
89SLV H 266 0.430 0.284 0.292
89SLV H1 267 0.451 0.436 0.311
90SLV O 268 0.452 1.549 1.148
90SLV H 269 0.435 1.615 1.221
90SLV H1 270 0.536 1.584 1.111
91SLV O 271 1.035 0.744 1.192
91SLV H 272 0.947 0.786 1.200
91SLV H1 273 1.048 0.696 1.278
92SLV O 274 1.212 0.540 0.521
92SLV H 275 1.265 0.529 0.440
92SLV H1 276 1.273 0.512 0.594
93SLV O 277 0.055 0.298 0.741
93SLV H 278 0.122 0.355 0.695
93SLV H1 279 0.074 0.208 0.704
94SLV O 280 1.508 0.750 1.536
94SLV H 281 1.476 0.672 1.589
94SLV H1 282 1.452 0.749 1.455
95SLV O 283 1.101 0.207 1.542
95SLV H 284 1.182 0.265 1.549
95SLV H1 285 1.089 0.174 0.011
96SLV O 286 1.545 1.382 0.002
96SLV H 287 1.595 1.305 0.040
96SLV H1 288 1.451 1.366 0.029
97SLV O 289 0.249 0.168 0.968
97SLV H 290 0.166 0.217 0.947
97SLV H1 291 0.237 0.146 1.065
98SLV O 292 1.550 0.968 1.221
98SLV H 293 1.581 1.041 1.163
98SLV H1 294 1.580 0.885 1.173
99SLV O 295 0.347 0.318 0.067
99SLV H 296 0.426 0.293 0.013
99SLV H1 297 0.368 0.410 0.096
100SLV O 298 0.772 0.512 1.384
100SLV H 299 0.858 0.483 1.343
100SLV H1 300 0.799 0.556 1.468
101URA C 301 1.001 1.134 1.184
101URA O 302 0.904 1.062 1.199
101URA N 303 0.982 1.268 1.152
101URA N1 304 1.122 1.080 1.143
101URA H 305 0.889 1.307 1.161
101URA H1 306 1.061 1.324 1.124
101URA H2 307 1.124 0.981 1.122
101URA H3 308 1.191 1.141 1.101
102URA C 309 0.825 0.251 0.476
102URA O 310 0.849 0.357 0.422
102URA N 311 0.913 0.145 0.461
102URA N1 312 0.693 0.213 0.493
102URA H 313 1.002 0.161 0.416
102URA H1 314 0.893 0.057 0.507
102URA H2 315 0.619 0.278 0.467
102URA H3 316 0.670 0.121 0.529
103URA C 317 0.809 0.916 1.509
103URA O 318 0.735 0.865 1.592
103URA N 319 0.944 0.884 1.507
103URA N1 320 0.779 1.044 1.463
103URA H 321 0.975 0.796 1.547
103URA H1 322 1.010 0.947 1.464
103URA H2 323 0.686 1.081 1.476
103URA H3 324 0.842 1.089 1.398
104URA C 325 1.539 0.966 0.252
104URA O 326 1.580 1.073 0.294
104URA N 327 1.478 0.963 0.128
104URA N1 328 1.606 0.851 0.288
104URA H 329 1.437 1.048 0.090
104URA H1 330 1.475 0.877 0.074
104URA H2 331 0.029 0.848 0.378
104URA H3 332 1.598 0.768 0.231
105URA C 333 0.821 0.466 0.100
105URA O 334 0.717 0.530 0.096
105URA N 335 0.940 0.528 0.066
105URA N1 336 0.818 0.330 0.075
105URA H 337 0.946 0.629 0.070
105URA H1 338 1.025 0.472 0.067
105URA H2 339 0.732 0.278 0.088
105URA H3 340 0.904 0.281 0.057
106URA C 341 0.799 0.777 0.906
106URA O 342 0.853 0.878 0.947
106URA N 343 0.812 0.743 0.772
106URA N1 344 0.682 0.733 0.966
106URA H 345 0.883 0.791 0.717
106URA H1 346 0.757 0.668 0.732
106URA H2 347 0.651 0.778 1.051
106URA H3 348 0.621 0.669 0.917
107URA C 349 0.984 0.919 0.438
107URA O 350 1.042 0.962 0.339
107URA N 351 0.856 0.966 0.467
107URA N1 352 1.006 0.787 0.475
107URA H 353 0.829 1.059 0.435
107URA H1 354 0.795 0.912 0.526
107URA H2 355 1.094 0.743 0.451
107URA H3 356 0.927 0.729 0.501
108URA C 357 0.804 1.476 0.729
108URA O 358 0.860 1.581 0.704
108URA N 359 0.737 1.462 0.850
108URA N1 360 0.857 1.357 0.682
108URA H 361 0.736 1.540 0.916
108URA H1 362 0.706 1.370 0.878
108URA H2 363 0.929 1.358 0.611
108URA H3 364 0.815 1.269 0.711
109URA C 365 1.417 0.821 0.607
109URA O 366 1.524 0.772 0.574
109URA N 367 1.355 0.915 0.526
109URA N1 368 1.389 0.833 0.742
109URA H 369 1.392 0.932 0.433
109URA H1 370 1.277 0.969 0.561
109URA H2 371 1.448 0.785 0.809
109URA H3 372 1.324 0.904 0.774
110URA C 373 0.688 0.161 1.094
110URA O 374 0.695 0.044 1.060
110URA N 375 0.583 0.238 1.047
110URA N1 376 0.732 0.196 1.221
110URA H 377 0.523 0.200 0.974
110URA H1 378 0.554 0.320 1.099
110URA H2 379 0.778 0.126 1.277
110URA H3 380 0.694 0.278 1.265
111URA C 381 1.024 0.365 0.838
111URA O 382 0.948 0.270 0.839
111URA N 383 1.155 0.348 0.879
111URA N1 384 1.002 0.470 0.751
111URA H 385 1.187 0.258 0.910
111URA H1 386 1.224 0.419 0.855
111URA H2 387 0.910 0.482 0.710
111URA H3 388 1.081 0.522 0.713
112URA C 389 0.185 0.559 0.510
112URA O 390 0.224 0.461 0.572
112URA N 391 0.062 0.553 0.446
112URA N1 392 0.223 0.685 0.553
112URA H 393 0.034 0.468 0.400
112URA H1 394 1.622 0.632 0.452
112URA H2 395 0.311 0.694 0.602
112URA H3 396 0.184 0.767 0.508
113URA C 397 0.447 1.024 0.469
113URA O 398 0.359 0.942 0.448
113URA N 399 0.414 1.145 0.529
113URA N1 400 0.553 1.031 0.380
113URA H 401 0.333 1.150 0.589
113URA H1 402 0.465 1.229 0.504
113URA H2 403 0.579 0.948 0.329
113URA H3 404 0.615 1.112 0.381
1.62280 1.62280 1.62280

File diff suppressed because it is too large Load Diff

@ -0,0 +1,28 @@
[ System ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270
271 272 273 274 275 276 277 278 279 280 281 282 283 284 285
286 287 288 289 290 291 292 293 294 295 296 297 298 299 300
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315
316 317 318 319 320 321 322 323 324 325 326 327 328 329 330
331 332 333 334 335 336 337 338 339 340 341 342 343 344 345
346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375
376 377 378 379 380 381 382 383 384 385 386 387 388 389 390
391 392 393 394 395 396 397 398 399 400 401 402 403 404

@ -0,0 +1,15 @@
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 5 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 0.7113990804113833 ; Short-range electrostatic cut-off
rvdw = 0.7113990804113833 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
;define = -DFLEXIBLE

@ -0,0 +1,41 @@
# This file was created Thu Apr 28 23:06:14 2022
# Created by:
# :-) GROMACS - gmx msd, 2021.3 (-:
#
# Executable: /home/adit/opt/gromacs-2021.3/build/bin/gmx
# Data prefix: /home/adit/opt/gromacs-2021.3 (source tree)
# Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
# Command line:
# gmx msd -f nvep.trr -s nvep.tpr -n SLV.ndx -o msd_SLV.xvg
# gmx msd is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@ title "Mean Square Displacement"
@ xaxis label "Time (ps)"
@ yaxis label "MSD (nm\S2\N)"
@TYPE xy
# MSD gathered over 5 ps with 1 restarts
# Diffusion constants fitted from time 0.5 to 4.5 ps
# D[(resname_SLV)] = 6.4232 (+/- 1.9949) (1e-5 cm^2/s)
0 0
0.25 0.0096222
0.5 0.0203094
0.75 0.0339887
1 0.0499902
1.25 0.0581352
1.5 0.0635697
1.75 0.0687521
2 0.0769021
2.25 0.0810643
2.5 0.0943307
2.75 0.107156
3 0.116171
3.25 0.12999
3.5 0.142552
3.75 0.155407
4 0.165951
4.25 0.169858
4.5 0.169497
4.75 0.175091
5 0.191759

@ -0,0 +1,41 @@
# This file was created Thu Apr 28 23:06:14 2022
# Created by:
# :-) GROMACS - gmx msd, 2021.3 (-:
#
# Executable: /home/adit/opt/gromacs-2021.3/build/bin/gmx
# Data prefix: /home/adit/opt/gromacs-2021.3 (source tree)
# Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
# Command line:
# gmx msd -f nvep.trr -s nvep.tpr -n URA.ndx -o msd_URA.xvg
# gmx msd is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@ title "Mean Square Displacement"
@ xaxis label "Time (ps)"
@ yaxis label "MSD (nm\S2\N)"
@TYPE xy
# MSD gathered over 5 ps with 1 restarts
# Diffusion constants fitted from time 0.5 to 4.5 ps
# D[(resname_URA)] = 3.9640 (+/- 3.7993) (1e-5 cm^2/s)
0 0
0.25 0.00908764
0.5 0.0186648
0.75 0.0266412
1 0.0334288
1.25 0.0384099
1.5 0.0487507
1.75 0.063285
2 0.0724394
2.25 0.0743349
2.5 0.082415
2.75 0.0883465
3 0.101314
3.25 0.103967
3.5 0.109389
3.75 0.110158
4 0.102565
4.25 0.101962
4.5 0.104766
4.75 0.114225
5 0.132007

@ -0,0 +1,407 @@
system
404
1SLV O 1 0.417 0.127 0.980 0.0096 0.4551 0.2395
1SLV H 2 0.443 0.046 1.028 -0.4908 0.0432 -0.1579
1SLV H1 3 0.367 0.090 0.905 -1.2084 1.4512 0.5314
2SLV O 4 0.719 0.022 0.013 0.1280 0.5902 0.3504
2SLV H 5 0.671 0.028 0.098 1.2760 -2.8160 1.4147
2SLV H1 6 0.663 0.061 -0.056 1.0934 -0.3243 -1.0145
3SLV O 7 0.435 0.495 1.480 -0.3386 0.2690 0.5433
3SLV H 8 0.417 0.581 1.438 0.4760 -0.0779 -0.5591
3SLV H1 9 0.358 0.448 1.445 -1.4587 2.6384 -0.3512
4SLV O 10 1.322 1.438 1.285 -0.0325 -0.0169 -0.8243
4SLV H 11 1.316 1.352 1.330 0.3368 -0.1374 -0.9969
4SLV H1 12 1.377 1.494 1.342 -1.0735 -0.0692 0.2606
5SLV O 13 0.402 1.125 0.779 -0.0377 0.1158 -0.0642
5SLV H 14 0.321 1.148 0.827 -1.8768 0.9213 -3.2358
5SLV H1 15 0.369 1.049 0.727 -0.4949 -0.1055 0.5324
6SLV O 16 0.639 0.468 1.242 0.2674 -0.0961 -0.1409
6SLV H 17 0.664 0.487 1.149 1.5826 -0.0697 0.1958
6SLV H1 18 0.623 0.560 1.269 -2.6264 -1.0511 1.8681
7SLV O 19 0.861 1.487 0.266 -0.3978 -0.0949 -0.4893
7SLV H 20 0.906 1.540 0.197 -0.6303 -0.6502 -1.0846
7SLV H1 21 0.786 1.437 0.230 -0.3109 0.2648 -1.1998
8SLV O 22 1.538 0.751 0.539 0.1567 -0.5353 0.0748
8SLV H 23 1.604 0.780 0.605 -1.4478 1.3947 0.9418
8SLV H1 24 1.459 0.781 0.588 2.3119 1.0293 2.9604
9SLV O 25 0.991 0.058 0.069 0.4452 -0.0407 0.1446
9SLV H 26 1.033 0.069 -0.018 -0.6858 0.9859 -0.3127
9SLV H1 27 0.897 0.065 0.043 0.0869 -1.0343 1.1053
10SLV O 28 1.526 1.482 0.351 0.2594 0.0315 0.4005
10SLV H 29 1.518 1.473 0.255 -1.6690 -0.7873 0.6042
10SLV H1 30 1.540 1.390 0.379 -0.6761 0.2682 1.7446
11SLV O 31 0.513 0.620 0.198 -0.3771 -0.3104 -0.6505
11SLV H 32 0.514 0.523 0.205 -0.4844 -0.2264 0.9926
11SLV H1 33 0.426 0.628 0.157 -0.8732 -1.4028 0.1449
12SLV O 34 1.080 0.064 0.800 0.5035 -0.2350 -0.0647
12SLV H 35 1.143 0.128 0.839 0.4072 0.4133 -0.9341
12SLV H1 36 1.039 0.120 0.731 1.0601 -1.9131 -1.8333
13SLV O 37 0.549 0.488 0.907 -0.2582 -0.2580 0.4263
13SLV H 38 0.603 0.430 0.850 -0.5852 0.9054 -1.1625
13SLV H1 39 0.526 0.558 0.843 2.9125 2.1792 1.6902
14SLV O 40 1.104 0.651 0.029 -0.3595 0.1544 -0.1572
14SLV H 41 1.020 0.607 0.050 -0.5154 0.3637 -0.3477
14SLV H1 42 1.083 0.704 -0.050 -0.7755 0.5042 0.1849
15SLV O 43 0.172 0.899 0.369 -0.7227 0.2668 -0.0252
15SLV H 44 0.170 0.977 0.310 0.5470 0.9305 0.7705
15SLV H1 45 0.106 0.837 0.332 -1.3565 0.4149 0.8235
16SLV O 46 0.755 0.257 0.228 -0.3553 -0.2597 0.1931
16SLV H 47 0.682 0.202 0.260 -2.5266 0.3928 -3.0851
16SLV H1 48 0.729 0.278 0.136 3.2523 -0.2798 -0.9832
17SLV O 49 1.197 1.014 0.727 0.1729 -0.4958 0.1763
17SLV H 50 1.125 1.041 0.667 -0.9245 -0.7593 1.3310
17SLV H1 51 1.192 0.917 0.725 -0.3712 -0.5005 1.0034
18SLV O 52 0.369 0.395 0.162 0.1065 0.0745 -0.3991
18SLV H 53 0.350 0.447 0.082 -0.9642 -0.4062 -0.4731
18SLV H1 54 0.281 0.368 0.195 0.6439 -0.1138 0.9323
19SLV O 55 1.443 1.126 0.028 0.1135 0.0053 -0.3157
19SLV H 56 1.419 1.124 0.122 -1.1332 1.2486 -0.5784
19SLV H1 57 1.500 1.204 0.016 -1.2280 0.8584 -1.3792
20SLV O 58 0.400 0.909 1.040 -0.0603 -0.1365 0.1969
20SLV H 59 0.439 0.994 1.068 -0.1259 0.4006 -1.2850
20SLV H1 60 0.313 0.898 1.083 -0.2452 -0.5801 -0.2853
21SLV O 61 0.581 0.882 0.818 0.4311 -1.0663 -0.9830
21SLV H 62 0.544 0.877 0.729 -0.2625 0.9368 -0.8471
21SLV H1 63 0.514 0.857 0.884 0.0203 -0.4787 -1.1776
22SLV O 64 1.286 0.044 1.079 -0.4598 0.3873 0.0889
22SLV H 65 1.342 0.047 1.159 1.8523 -1.0161 -1.3469
22SLV H1 66 1.293 -0.047 1.044 -0.1445 0.4756 -0.0780
23SLV O 67 0.620 0.256 0.776 0.3699 -0.9281 -0.6039
23SLV H 68 0.614 0.192 0.703 0.0159 -0.0901 -1.3425
23SLV H1 69 0.526 0.273 0.793 -0.0659 -0.5172 -3.0261
24SLV O 70 0.387 1.212 0.073 -0.3622 -0.3313 -0.2897
24SLV H 71 0.477 1.241 0.050 -0.3379 -0.0441 0.1595
24SLV H1 72 0.354 1.285 0.127 -0.0132 1.4680 -2.3509
25SLV O 73 1.541 0.480 0.480 0.3597 0.1768 -0.3088
25SLV H 74 1.539 0.571 0.515 -1.2563 0.5264 -1.2041
25SLV H1 75 1.551 0.415 0.551 2.5780 0.3991 -0.3449
26SLV O 76 0.592 0.049 0.560 0.0861 0.2554 -0.4392
26SLV H 77 0.560 0.127 0.512 -1.2016 0.7678 1.1630
26SLV H1 78 0.689 0.047 0.554 0.3344 3.9848 0.1508
27SLV O 79 0.941 0.759 1.233 0.7787 -0.2728 0.0255
27SLV H 80 0.942 0.840 1.287 -0.2767 -0.3672 0.1941
27SLV H1 81 0.985 0.794 1.153 -1.2311 -0.5031 -1.2457
28SLV O 82 1.606 0.051 0.564 -0.6492 -0.3493 -0.2911
28SLV H 83 1.614 0.002 0.480 -0.1535 -0.2180 -0.3253
28SLV H1 84 1.624 -0.025 0.623 -0.0484 1.0302 1.3988
29SLV O 85 0.231 1.359 0.502 -0.5673 -0.0158 0.2291
29SLV H 86 0.295 1.367 0.575 0.6003 -0.3462 -0.7283
29SLV H1 87 0.260 1.280 0.454 -0.3100 -0.1226 0.5604
30SLV O 88 1.451 0.218 0.911 0.2817 0.1732 0.3031
30SLV H 89 1.437 0.125 0.935 1.3627 -0.7664 -2.3566
30SLV H1 90 1.364 0.261 0.912 0.8276 1.3520 -0.2257
31SLV O 91 0.858 0.758 0.134 -0.2391 -0.1526 -0.2981
31SLV H 92 0.948 0.722 0.147 0.4904 1.8502 0.6419
31SLV H1 93 0.820 0.690 0.075 1.9418 -2.0834 0.3517
32SLV O 94 0.244 0.233 0.587 0.2567 0.1140 0.9333
32SLV H 95 0.213 0.251 0.677 -0.0448 0.2118 0.8079
32SLV H1 96 0.155 0.218 0.551 1.0318 -0.5142 -0.9045
33SLV O 97 1.384 1.463 0.870 0.5901 0.1708 -0.1402
33SLV H 98 1.370 1.449 0.775 0.4862 -0.1746 -0.0729
33SLV H1 99 1.356 1.376 0.904 -0.6637 0.4360 -0.4611
34SLV O 100 0.818 0.259 1.250 -0.0992 -0.2427 -0.4532
34SLV H 101 0.784 0.349 1.264 -1.6038 -0.7238 -0.8583
34SLV H1 102 0.802 0.244 1.155 -0.4422 1.6993 -0.7440
35SLV O 103 0.715 0.686 0.380 -0.0193 0.1075 -0.4958
35SLV H 104 0.642 0.652 0.326 -0.8190 1.8351 -0.5785
35SLV H1 105 0.795 0.655 0.334 -0.3895 -0.9614 -0.4344
36SLV O 106 0.925 1.361 1.147 -0.3659 -0.0627 -0.0861
36SLV H 107 0.950 1.453 1.125 -2.2485 0.6056 0.3796
36SLV H1 108 0.912 1.363 1.244 -0.7789 -1.1401 -0.1176
37SLV O 109 0.656 1.444 1.069 0.1223 0.2291 -0.2527
37SLV H 110 0.709 1.525 1.060 0.4109 0.2744 1.5304
37SLV H1 111 0.721 1.378 1.039 0.2843 0.0697 0.4342
38SLV O 112 0.132 1.161 0.066 -0.5492 -0.1295 -0.1570
38SLV H 113 0.226 1.180 0.050 -0.4262 2.8143 2.9078
38SLV H1 114 0.119 1.067 0.047 0.5610 0.2824 -3.6320
39SLV O 115 0.945 0.162 0.564 0.2369 -0.4457 0.1589
39SLV H 116 0.950 0.189 0.471 -1.2440 -2.0288 -0.4412
39SLV H1 117 0.947 0.251 0.604 0.6771 -1.1453 1.7686
40SLV O 118 0.001 0.680 0.229 0.0960 -0.0981 -0.3446
40SLV H 119 -0.004 0.651 0.322 3.6845 0.1325 0.0535
40SLV H1 120 -0.070 0.637 0.179 -1.1751 0.3847 0.9620
41SLV O 121 0.092 1.357 1.069 -0.1724 0.2945 0.9680
41SLV H 122 0.188 1.370 1.075 0.1731 -1.4604 -0.0291
41SLV H1 123 0.072 1.279 1.124 3.3827 -2.1762 -0.8230
42SLV O 124 0.581 1.587 0.264 0.0761 -0.1106 -0.1031
42SLV H 125 0.606 1.496 0.288 -0.8008 -0.0347 1.1507
42SLV H1 126 0.519 1.602 0.337 0.9651 -1.3560 0.9537
43SLV O 127 0.093 0.932 1.024 -0.3827 0.2486 0.0086
43SLV H 128 0.063 1.012 1.071 1.4086 -0.1269 1.8990
43SLV H1 129 0.076 0.952 0.930 0.4391 -1.2472 -0.4837
44SLV O 130 0.885 1.431 1.414 -0.6600 0.6425 0.4699
44SLV H 131 0.824 1.449 1.488 -0.0933 0.3436 1.0182
44SLV H1 132 0.932 1.513 1.394 -0.4775 0.5194 0.3911
45SLV O 133 1.444 0.452 1.080 -0.2396 0.3501 0.3150
45SLV H 134 1.505 0.465 1.155 0.5154 0.1051 -0.2493
45SLV H1 135 1.496 0.392 1.024 -1.3159 0.3942 -0.7752
46SLV O 136 0.385 1.336 1.068 0.0801 0.2112 -0.7873
46SLV H 137 0.422 1.246 1.060 1.0491 0.5569 -0.4114
46SLV H1 138 0.463 1.394 1.073 -1.4488 2.2965 1.2502
47SLV O 139 1.015 0.809 0.893 0.4886 0.1851 0.7985
47SLV H 140 0.946 0.850 0.839 -0.6531 -0.9223 1.3671
47SLV H1 141 1.037 0.887 0.947 -0.1378 -0.0209 1.3740
48SLV O 142 0.636 0.367 1.603 -0.8413 -0.2207 0.4040
48SLV H 143 0.578 0.442 1.579 -0.1368 -0.3688 -1.9657
48SLV H1 144 0.595 0.300 1.546 1.3194 -0.7535 -0.6174
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49SLV H 146 0.649 1.220 1.478 0.8536 -2.2547 1.4769
49SLV H1 147 0.652 1.174 1.620 -0.7048 1.6490 3.0082
50SLV O 148 0.049 1.488 0.788 0.0520 0.7816 -0.3860
50SLV H 149 -0.045 1.488 0.811 0.7934 1.2247 3.2905
50SLV H1 150 0.079 1.442 0.868 2.6303 2.5790 -0.1884
51SLV O 151 1.551 0.296 0.670 -0.1567 0.1572 -0.4597
51SLV H 152 1.570 0.204 0.647 -0.2677 0.3447 -1.3228
51SLV H1 153 1.524 0.307 0.763 0.9149 1.1666 -0.2468
52SLV O 154 1.222 1.260 1.003 -0.4894 0.1313 -0.1158
52SLV H 155 1.192 1.228 1.090 -0.2107 -0.4777 -0.2379
52SLV H1 156 1.183 1.202 0.935 -3.5554 0.5758 1.1078
53SLV O 157 1.019 0.116 1.379 -0.2842 0.1889 -0.6209
53SLV H 158 0.949 0.153 1.323 -1.1557 3.3400 2.2041
53SLV H1 159 1.056 0.194 1.424 -0.6420 1.4595 -2.4787
54SLV O 160 0.865 0.503 1.575 -0.6741 -0.2135 -0.2107
54SLV H 161 0.918 0.509 1.494 -1.4508 -0.7899 -0.7805
54SLV H1 162 0.781 0.457 1.561 0.2942 -1.5090 -2.0446
55SLV O 163 0.744 1.028 0.206 1.1241 -0.0516 -0.6999
55SLV H 164 0.721 1.040 0.300 2.2062 -1.0825 -0.2838
55SLV H1 165 0.802 0.950 0.205 0.8105 -0.3366 -3.2291
56SLV O 166 0.621 1.294 0.294 0.2888 -0.3004 0.5213
56SLV H 167 0.624 1.287 0.391 -2.6902 -2.0187 0.6153
56SLV H1 168 0.677 1.217 0.276 0.8961 0.6453 -2.1121
57SLV O 169 0.904 0.406 0.394 -0.4767 -0.3917 0.1895
57SLV H 170 0.852 0.367 0.322 -0.6687 -0.1093 0.1706
57SLV H1 171 0.982 0.402 0.336 -1.3175 -0.5368 -0.9677
58SLV O 172 0.570 0.165 1.416 0.1642 0.6279 0.7554
58SLV H 173 0.650 0.171 1.361 0.1737 -2.9944 0.1409
58SLV H1 174 0.512 0.139 1.343 0.2429 -0.1019 0.9418
59SLV O 175 0.898 0.529 1.061 0.2209 0.0585 -0.7310
59SLV H 176 0.874 0.604 1.118 -2.4702 -0.0078 -1.6362
59SLV H1 177 0.934 0.571 0.981 0.4211 -2.3786 -2.0129
60SLV O 178 0.193 0.667 1.035 0.2375 -0.0210 0.0761
60SLV H 179 0.273 0.689 0.985 -0.6329 -0.4310 -1.5734
60SLV H1 180 0.140 0.744 1.009 2.0547 1.0957 -0.5144
61SLV O 181 0.805 0.554 0.621 -0.0831 -0.0941 -0.4297
61SLV H 182 0.747 0.629 0.600 -3.0796 -1.5821 1.7484
61SLV H1 183 0.826 0.504 0.540 -0.1483 -1.0185 0.1071
62SLV O 184 0.251 0.686 0.089 -0.2305 0.7897 0.2082
62SLV H 185 0.293 0.774 0.090 1.2929 0.1432 3.0082
62SLV H1 186 0.181 0.687 0.156 -0.7567 1.6576 -0.3382
63SLV O 187 0.325 1.560 0.724 0.8732 -0.1267 0.6394
63SLV H 188 0.232 1.532 0.726 0.5598 0.8792 1.7625
63SLV H1 189 0.341 1.595 0.635 -2.7243 0.6835 0.1457
64SLV O 190 0.443 0.913 0.057 -0.0238 0.9076 -0.1754
64SLV H 191 0.441 1.004 0.093 0.2850 1.2658 -1.0377
64SLV H1 192 0.521 0.873 0.099 -0.5431 0.5584 0.4725
65SLV O 193 1.424 1.413 0.097 0.7207 -0.4988 -0.6572
65SLV H 194 1.480 1.447 0.025 1.2852 -1.1812 -0.5535
65SLV H1 195 1.335 1.416 0.057 0.1388 0.4108 0.6620
66SLV O 196 1.160 0.346 1.498 -0.3278 -0.0786 0.0058
66SLV H 197 1.208 0.322 1.417 -0.5693 2.4627 -0.9634
66SLV H1 198 1.122 0.435 1.493 -1.0302 -0.2374 1.7463
67SLV O 199 0.949 0.024 1.074 -0.0188 0.1663 -0.3720
67SLV H 200 0.905 0.101 1.034 3.3370 2.1653 -0.5734
67SLV H1 201 1.044 0.029 1.054 0.8053 -2.4039 2.0587
68SLV O 202 0.372 0.316 1.244 -0.3735 -0.0436 0.5759
68SLV H 203 0.451 0.354 1.286 0.2221 1.0977 -1.4446
68SLV H1 204 0.380 0.329 1.148 -0.0455 1.3813 0.7646
69SLV O 205 0.589 1.114 1.008 0.2236 0.6814 0.4148
69SLV H 206 0.680 1.079 1.009 -0.4420 -1.7408 -3.3258
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70SLV O 208 0.028 0.642 1.497 -0.0382 0.1164 0.1914
70SLV H 209 0.011 0.729 1.538 -0.7111 0.2225 -0.2939
70SLV H1 210 0.114 0.617 1.535 -0.0104 0.9358 0.6882
71SLV O 211 0.184 0.903 0.648 0.2298 0.2313 0.2388
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71SLV H1 213 0.196 0.894 0.551 -2.3552 -0.9450 -0.0505
72SLV O 214 1.125 1.346 0.195 0.5020 -0.2966 0.2713
72SLV H 215 1.042 1.335 0.244 0.0398 0.4111 -0.3277
72SLV H1 216 1.183 1.280 0.237 0.6972 -0.8094 -0.7552
73SLV O 217 1.094 0.339 0.176 -0.3651 0.3835 -0.2826
73SLV H 218 1.088 0.242 0.164 0.3162 0.3128 -0.1316
73SLV H1 219 1.134 0.361 0.090 -1.0753 0.3460 -0.6279
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74SLV H 221 1.650 1.602 1.471 -2.0316 2.2885 -0.7727
74SLV H1 222 1.624 1.616 1.617 -0.6530 0.9866 -0.5657
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75SLV H 224 1.303 0.403 1.174 -0.2868 0.7595 -0.2432
75SLV H1 225 1.226 0.279 1.164 1.4203 1.1354 -1.8104
76SLV O 226 1.568 1.587 1.183 -0.2289 -0.0571 -0.2412
76SLV H 227 1.619 1.655 1.231 -1.5843 1.2428 -0.5436
76SLV H1 228 1.628 1.517 1.155 0.3999 -0.7721 2.5712
77SLV O 229 0.236 0.307 0.859 0.2327 0.1063 -0.3146
77SLV H 230 0.234 0.404 0.871 -2.1417 0.2111 -0.9996
77SLV H1 231 0.282 0.258 0.930 0.6356 0.7263 -0.1407
78SLV O 232 0.883 1.127 0.975 -0.6636 -0.5569 0.0713
78SLV H 233 0.872 1.198 0.909 -1.4791 -1.3323 -0.6436
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79SLV O 235 1.348 1.469 0.575 0.0966 -0.5109 -0.3660
79SLV H 236 1.416 1.465 0.506 0.3599 -1.0393 -0.0802
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80SLV O 238 0.469 0.244 0.379 0.1423 0.3769 0.2450
80SLV H 239 0.395 0.279 0.432 -0.4969 0.3356 -0.6075
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81SLV H1 243 0.119 1.242 0.346 1.3196 -0.2447 -4.4026
82SLV O 244 0.038 0.914 0.022 0.4152 0.1796 0.3062
82SLV H 245 -0.007 0.862 0.091 1.3043 0.6054 1.2381
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83SLV H1 249 1.373 1.117 1.457 1.8993 1.7000 0.5553
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84SLV H 251 0.987 0.620 1.326 1.3296 -0.1576 -0.4082
84SLV H1 252 1.056 0.487 1.275 -0.0245 1.8983 -1.1221
85SLV O 253 0.842 0.932 0.712 0.2784 -0.2916 0.8856
85SLV H 254 0.757 0.941 0.758 -0.8045 -1.7571 -0.7145
85SLV H1 255 0.868 1.021 0.681 -1.2820 -0.2188 -0.2953
86SLV O 256 1.502 0.749 0.923 -0.4231 0.0506 -0.0955
86SLV H 257 1.467 0.665 0.957 0.0690 -0.0829 0.0800
86SLV H1 258 1.509 0.800 1.005 0.6109 0.2405 -0.2877
87SLV O 259 0.082 0.484 1.239 0.1270 0.1994 0.4403
87SLV H 260 0.166 0.476 1.287 -0.7210 -1.1246 1.7920
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88SLV O 262 0.339 1.123 0.395 0.4318 0.3781 0.1365
88SLV H 263 0.427 1.129 0.355 1.5419 0.6141 2.4535
88SLV H1 264 0.334 1.037 0.439 -0.5702 0.0587 -0.5592
89SLV O 265 0.112 0.330 1.566 0.0236 -0.2344 0.1254
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89SLV H1 267 0.072 0.259 1.513 0.4227 -0.1161 -0.3452
90SLV O 268 1.206 0.034 0.223 -0.1913 -0.3740 0.1450
90SLV H 269 1.186 -0.049 0.268 0.1728 -1.1733 -1.0982
90SLV H1 270 1.125 0.038 0.169 -0.5301 -0.6826 0.6305
91SLV O 271 1.537 1.140 1.128 -0.1243 0.1797 0.0380
91SLV H 272 1.489 1.155 1.211 1.1433 -1.6040 1.1443
91SLV H1 273 1.496 1.205 1.068 -2.0301 0.5032 1.5654
92SLV O 274 0.107 0.343 0.288 -0.3657 -0.0142 0.5871
92SLV H 275 0.035 0.390 0.334 -1.3139 0.6797 -1.4530
92SLV H1 276 0.072 0.350 0.197 -0.5920 1.0725 0.7385
93SLV O 277 0.619 0.784 1.258 -0.1269 0.5489 -0.6407
93SLV H 278 0.666 0.869 1.249 -0.5109 1.0133 1.3862
93SLV H1 279 0.524 0.794 1.238 0.2461 3.0842 -1.5339
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94SLV H 281 0.676 1.273 1.210 -1.4227 -0.4710 -0.3330
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95SLV O 283 0.703 1.043 0.473 0.3633 -0.3263 -0.6092
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96SLV O 286 0.329 0.717 1.362 0.1846 0.0893 0.2050
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97SLV O 289 0.813 0.276 0.983 -0.3136 -0.2974 -0.5314
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98SLV O 292 1.379 0.663 0.053 0.8752 -0.2691 0.1940
98SLV H 293 1.283 0.648 0.057 0.9076 -0.3285 1.0814
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99SLV O 295 0.501 0.850 0.497 -0.6879 -0.5108 -0.3080
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100SLV O 298 0.121 0.155 1.333 -0.0746 0.1646 0.3513
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100SLV H1 300 0.200 0.098 1.328 2.0722 3.0097 -1.0335
101URA C 301 0.978 1.057 1.465 0.5186 -0.6762 0.0356
101URA O 302 0.925 0.990 1.381 -0.7547 0.3130 -0.1151
101URA N 303 1.045 1.171 1.428 0.5217 -0.1084 -0.2729
101URA N1 304 1.002 1.012 1.595 -0.1880 -0.7418 -0.0572
101URA H 305 1.038 1.245 1.497 -0.4156 -1.8273 1.5852
101URA H1 306 1.039 1.198 1.331 1.4714 -0.9022 -0.5685
101URA H2 307 1.005 0.915 1.626 -0.3759 -0.4129 1.0251
101URA H3 308 1.051 1.067 1.665 -1.5822 -0.8644 1.0586
102URA C 309 0.217 1.585 0.231 0.6627 -0.2886 0.4185
102URA O 310 0.231 1.465 0.206 -0.0212 -0.4249 0.2371
102URA N 311 0.275 1.680 0.148 0.4966 -0.1491 -0.6895
102URA N1 312 0.246 1.623 0.360 1.0090 0.0248 -0.1690
102URA H 313 0.338 1.660 0.072 2.1924 2.9388 -0.2754
102URA H1 314 0.267 1.775 0.184 1.2159 -0.7159 1.0862
102URA H2 315 0.212 1.581 0.445 0.0430 -0.0851 -0.6052
102URA H3 316 0.320 1.692 0.369 1.6294 -0.5789 -0.4684
103URA C 317 1.406 0.289 0.138 0.1830 0.0527 0.5427
103URA O 318 1.448 0.403 0.118 -0.1782 0.2971 -0.0852
103URA N 319 1.420 0.235 0.261 0.2644 0.0721 -0.1557
103URA N1 320 1.378 0.207 0.040 0.7288 0.1636 -0.1851
103URA H 321 1.369 0.151 0.287 0.4454 0.1414 0.4439
103URA H1 322 1.485 0.280 0.324 -0.7300 1.4887 -0.1015
103URA H2 323 1.324 0.124 0.061 0.0294 0.4812 -0.6430
103URA H3 324 1.375 0.237 -0.057 -0.8275 -1.2400 -0.6216
104URA C 325 1.073 1.288 0.573 -0.2033 0.1915 -0.4414
104URA O 326 1.050 1.183 0.520 0.0193 0.0392 0.6733
104URA N 327 1.003 1.396 0.530 -0.3408 -0.7506 -0.2316
104URA N1 328 1.120 1.291 0.707 -0.5285 -0.3004 0.5376
104URA H 329 1.063 1.478 0.529 -1.1807 -0.1315 -1.2600
104URA H1 330 0.936 1.391 0.454 -0.7560 1.8498 -0.1342
104URA H2 331 1.135 1.385 0.742 -2.5868 0.8710 -1.4669
104URA H3 332 1.134 1.206 0.759 -0.0139 0.0940 1.0641
105URA C 333 1.148 0.422 0.828 0.2550 0.2836 -0.0506
105URA O 334 1.212 0.334 0.885 -0.1361 0.0485 -0.0782
105URA N 335 1.017 0.392 0.796 -0.3636 0.0375 0.1769
105URA N1 336 1.183 0.552 0.842 0.2617 -0.2344 -0.1390
105URA H 337 0.951 0.464 0.771 -1.8921 -1.2918 0.2448
105URA H1 338 0.980 0.306 0.833 -0.0890 -0.6229 -1.0296
105URA H2 339 1.279 0.571 0.871 0.6963 -1.6770 -0.5306
105URA H3 340 1.113 0.625 0.840 0.7178 0.2064 -2.2772
106URA C 341 0.353 0.601 0.650 0.3699 -0.0084 -0.4782
106URA O 342 0.444 0.669 0.696 0.8196 -0.1082 -0.4689
106URA N 343 0.371 0.511 0.549 -0.4884 -0.5214 0.3211
106URA N1 344 0.236 0.588 0.724 -0.3603 0.4174 0.6259
106URA H 345 0.328 0.419 0.557 1.1026 -1.4330 -1.0297
106URA H1 346 0.465 0.511 0.512 0.0476 -1.8382 1.5808
106URA H2 347 0.208 0.660 0.789 0.3845 -1.3767 3.0632
106URA H3 348 0.175 0.513 0.692 -0.5853 0.5600 0.7185
107URA C 349 0.715 1.319 0.707 0.2259 0.2319 0.3996
107URA O 350 0.781 1.229 0.662 0.0647 0.1405 0.1940
107URA N 351 0.772 1.443 0.716 0.2243 -0.0957 -0.2087
107URA N1 352 0.582 1.316 0.661 -0.0518 -0.1852 -0.3747
107URA H 353 0.869 1.461 0.738 0.9211 0.4312 -3.1718
107URA H1 354 0.709 1.521 0.703 0.6363 0.0251 -1.7841
107URA H2 355 0.539 1.402 0.628 -1.4271 -0.5498 0.3920
107URA H3 356 0.519 1.245 0.696 0.7532 -0.9754 -0.5188
108URA C 357 0.370 1.530 1.372 -0.2147 0.5102 0.3457
108URA O 358 0.372 1.606 1.275 -0.2529 -0.4120 0.3821
108URA N 359 0.472 1.433 1.381 -1.0163 -0.2686 0.5039
108URA N1 360 0.297 1.542 1.489 0.1137 -0.2283 -0.0001
108URA H 361 0.548 1.421 1.315 -0.3939 0.2991 1.0946
108URA H1 362 0.497 1.401 1.474 -1.0800 1.4877 1.1769
108URA H2 363 0.290 1.459 1.547 -0.4451 -0.1051 0.1115
108URA H3 364 0.254 1.631 1.509 2.1984 1.0090 -0.7758
109URA C 365 1.283 0.950 0.305 -0.3541 -0.5064 -0.0044
109URA O 366 1.228 1.011 0.212 -0.8582 0.3405 -0.1269
109URA N 367 1.343 1.029 0.407 0.7883 -0.3652 0.6695
109URA N1 368 1.360 0.840 0.278 -0.0668 0.3900 -0.8395
109URA H 369 1.376 0.968 0.480 -0.9852 -0.5569 1.3611
109URA H1 370 1.354 1.130 0.409 0.0901 -0.2943 1.3088
109URA H2 371 1.349 0.802 0.185 -0.9798 -0.8108 -0.2660
109URA H3 372 1.418 0.790 0.345 -0.9775 -1.4354 -1.3435
110URA C 373 1.372 0.800 1.287 -0.2143 0.6357 0.4104
110URA O 374 1.312 0.901 1.260 0.2246 -0.3347 0.8551
110URA N 375 1.299 0.682 1.296 -0.3068 0.2309 0.1095
110URA N1 376 1.512 0.784 1.263 0.5829 -0.3621 -0.6706
110URA H 377 1.199 0.676 1.282 -0.2990 -2.3093 0.5795
110URA H1 378 1.358 0.601 1.313 -0.7588 0.1592 1.5081
110URA H2 379 1.559 0.874 1.269 0.7354 -0.2333 -2.8811
110URA H3 380 1.550 0.701 1.305 -0.3966 -1.2917 -1.5639
111URA C 381 0.275 1.120 1.326 0.5616 0.5738 -0.1880
111URA O 382 0.231 1.003 1.333 0.5129 0.3466 -0.4642
111URA N 383 0.396 1.147 1.383 -0.2619 -0.1984 0.1075
111URA N1 384 0.178 1.214 1.331 -0.0276 0.2031 0.7369
111URA H 385 0.440 1.234 1.356 0.1174 -0.0009 1.3273
111URA H1 386 0.444 1.091 1.452 -0.0341 0.4363 0.4763
111URA H2 387 0.084 1.187 1.356 -1.9017 3.1675 -2.2967
111URA H3 388 0.207 1.302 1.373 -1.1803 0.4332 1.0875
112URA C 389 1.187 0.671 0.535 0.5074 -0.3318 -0.0162
112URA O 390 1.260 0.753 0.591 0.2056 0.1168 0.2518
112URA N 391 1.061 0.710 0.487 -0.2898 -0.3490 0.1816
112URA N1 392 1.244 0.578 0.453 -0.2985 0.2997 0.5757
112URA H 393 1.048 0.806 0.455 -0.2645 0.2546 1.8846
112URA H1 394 0.994 0.637 0.467 -1.8273 1.2608 -0.8190
112URA H2 395 1.195 0.515 0.390 1.1268 -0.4552 0.1924
112URA H3 396 1.344 0.567 0.456 -0.3351 -0.6010 -0.6117
113URA C 397 1.551 1.137 0.754 0.3728 1.2113 0.4130
113URA O 398 1.673 1.138 0.760 0.4830 -0.0422 0.1989
113URA N 399 1.486 1.014 0.777 -0.0825 0.3621 0.0796
113URA N1 400 1.493 1.219 0.654 -0.4069 0.1890 0.2794
113URA H 401 1.524 0.936 0.829 -2.6709 -2.1558 -1.5287
113URA H1 402 1.385 1.018 0.772 -0.1551 0.4102 1.3328
113URA H2 403 1.413 1.181 0.604 1.0092 1.1549 -3.0095
113URA H3 404 1.557 1.281 0.605 1.0733 -0.6395 1.1018
1.60651 1.60651 1.60651

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title = NPT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 100000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 0.7113990804113833 ; short-range electrostatic cutoff (in nm)
rvdw = 0.7113990804113833 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 298.15 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Berendsen ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off

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