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CMMDE
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change -slurm to -q

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Aditya Wibawa Sakti 1 year ago
parent 0564066980
commit b316af7e71
2 changed files with 40 additions and 36 deletions
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  1. 35
      bin/cmmde.py
  2. 41
      lib/cmmde_solution.py

35
bin/cmmde.py
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@ -58,6 +58,7 @@ parser.add_argument('-ct', '--c_terlarut', type=str, help='Muatan bersih molekul
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('-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('-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('-l', '--lapang', type=float, default=5, help='Panjang tambahan (Angstrom) pada rusuk kubus untuk menghindari bad contact. Default: 10.0.')
parser.add_argument('-rc','--rcol',type=float,default=0, help='Additional Coulombic radius for PME calculation')
parser.add_argument('-gen','--generate_dftbinp',type=str,default='false',help='Apakah ingin mengkonversi ke dalam format koordinat xyz?') 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('-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('-nequil','--nequil',type=int, default=50000, help='Jumlah step pada saat ekuilibrasi.')
@ -180,7 +181,7 @@ parser.add_argument('-cpress','--cellpress',type=float,default=0.0,help='Tekanan
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('-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('-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.') 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.')
parser.add_argument("-slurm","--slurm",type=str,default="true",help="Apakah akan menggunakan slurm atau tidak. Default: true") parser.add_argument("-q","--queue",type=str,default="true",help="Apakah akan menggunakan sistem antrian atau tidak. Default: true")
opt=parser.parse_args(sys.argv[1:]) opt=parser.parse_args(sys.argv[1:])
@ -188,7 +189,7 @@ opt=parser.parse_args(sys.argv[1:])
if ('.xyz' or '.pdb' or 'POSCAR' or '.vasp' or '.poscar') in opt.input: if ('.xyz' or '.pdb' or 'POSCAR' or '.vasp' or '.poscar') in opt.input:
geom = opt.input geom = opt.input
elif '.mol2' in opt.input: elif '.mol2' in opt.input:
if opt.slurm == "true": if opt.queue == "true":
with open('run_babel.sh','w') as fout: with open('run_babel.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -210,7 +211,7 @@ obabel {} -O geom.xyz""".format(opt.nproc,opt.input),file=fout)
geom = 'geom.xyz' 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): 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)) os.system("echo '{}' > geom.smi".format(opt.input))
if opt.slurm == "true": if opt.queue == "true":
with open('run_babel.sh','w') as fout: with open('run_babel.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -255,7 +256,7 @@ if opt.software == 'dock':
addcharge(opt.input,opt.chargetype) addcharge(opt.input,opt.chargetype)
if opt.job == 'sphgen': if opt.job == 'sphgen':
sphgen(opt.input) sphgen(opt.input)
if opt.slurm == 'true': if opt.queue == 'true':
with open('run_sphgen.sh','w') as fout: with open('run_sphgen.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -280,7 +281,7 @@ $DOCK_DIR/sphere_selector protein.sph {} {}""".format(opt.nproc,opt.ligand,opt.d
showsphere() showsphere()
if opt.job == 'gridgen': if opt.job == 'gridgen':
gridgen(opt.input) gridgen(opt.input)
if opt.slurm == "true": if opt.queue == "true":
with open('run_grid.sh','w') as fout: with open('run_grid.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -302,7 +303,7 @@ $DOCK_DIR/sphere_selector protein.sph {} {}""".format(opt.nproc,opt.ligand,opt.d
if opt.job == 'rigiddock': if opt.job == 'rigiddock':
rigiddock(opt.ligand,opt.calcrmsd) rigiddock(opt.ligand,opt.calcrmsd)
if opt.slurm == "true": if opt.queue == "true":
with open('run_rigiddock.sh','w') as fout: with open('run_rigiddock.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -323,7 +324,7 @@ $DOCK_DIR/sphere_selector protein.sph {} {}""".format(opt.nproc,opt.ligand,opt.d
os.system("./run_rigiddock.sh") os.system("./run_rigiddock.sh")
if opt.job == 'flexdock': if opt.job == 'flexdock':
flexdock(opt.ligand,opt.calcrmsd) flexdock(opt.ligand,opt.calcrmsd)
if opt.slurm == "true": if opt.queue == "true":
with open('run_flexdock.sh','w') as fout: with open('run_flexdock.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -367,7 +368,7 @@ if opt.software == 'dftb':
geom = 'in.gen' geom = 'in.gen'
dftb(geom,opt.job,opt.activeatoms,opt.method,opt.parapath,opt.dispersion,opt.kpts,opt.hcorr) dftb(geom,opt.job,opt.activeatoms,opt.method,opt.parapath,opt.dispersion,opt.kpts,opt.hcorr)
if opt.slurm == "true": if opt.queue == "true":
with open('run.sh','w') as fout: with open('run.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -395,7 +396,7 @@ if opt.software == 'qe':
# RUNNING SCRIPT # RUNNING SCRIPT
if opt.software == 'orca': if opt.software == 'orca':
if opt.slurm=="true": if opt.queue=="true":
with open('run.sh','w') as fout: with open('run.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -416,7 +417,7 @@ if opt.software == 'orca':
os.system("chmod +x run.sh") os.system("chmod +x run.sh")
os.system('./run.sh') os.system('./run.sh')
if opt.software == 'nwchem': if opt.software == 'nwchem':
if opt.slurm=="true": if opt.queue=="true":
with open('run.sh','w') as fout: with open('run.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
@ -449,7 +450,7 @@ mpirun -np {} $QE_COMMAND < cmmd.in > cmmd.out""".format(opt.nproc,opt.nproc),fi
os.system('sbatch run.sh') os.system('sbatch run.sh')
if opt.software == 'dcdftb': if opt.software == 'dcdftb':
if opt.slurm == 'true': if opt.queue == 'true':
os.system("cp cmmd.in dftb.inp") os.system("cp cmmd.in dftb.inp")
with open('run.sh','w') as fout: with open('run.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
@ -477,23 +478,23 @@ fi""",file=fout)
os.system('./run.sh') os.system('./run.sh')
if opt.software == 'gromacs': if opt.software == 'gromacs':
if opt.slurm == 'true': if opt.queue == 'true':
with open('run.sh','w') as fout: with open('run.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
#SBATCH --ntasks=1 #SBATCH --ntasks=1
#SBATCH --cpus-per-task=1 #SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0 #SBATCH --time=168:0:0
export OMP_NUM_THREADS={} export OMP_NUM_THREADS=1
cd $PWD cd $PWD
$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {}""".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,opt.nnpt,opt.compress),file=fout) $GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {} -np {}""".format(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,opt.nnpt,opt.compress,opt.nproc,opt.rcol),file=fout)
os.system('sbatch run.sh') os.system('sbatch run.sh')
else: else:
with open('run.sh','w') as fout: with open('run.sh','w') as fout:
print("""#!/bin/bash print("""#!/bin/bash
export OMP_NUM_THREADS={} export OMP_NUM_THREADS=1
cd $PWD cd $PWD
$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {}""".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,opt.nnpt,opt.compress),file=fout) $GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {} -np {}""".format(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,opt.nnpt,opt.compress,opt.nproc,opt.rcol),file=fout)
os.system('chmod +x run.sh') os.system('chmod +x run.sh')
os.system('./run.sh') os.system('./run.sh')
@ -505,4 +506,4 @@ if opt.job == 'ligprep' and opt.software == 'gmx':
# Program XTB Standalone # Program XTB Standalone
if opt.software == 'xtb': if opt.software == 'xtb':
xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan,opt.solvent,opt.charge,opt.mult,opt.method,opt.fixedatoms,opt.fixedelements,opt.slurm) xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan,opt.solvent,opt.charge,opt.mult,opt.method,opt.fixedatoms,opt.fixedelements,opt.queue)

41
lib/cmmde_solution.py
Unescape View File

@ -30,6 +30,8 @@ parser.add_argument('--packmol', type=str, default='/Users/adit/opt/packmol/pack
parser.add_argument('-l','--lapang',type=float, default=5, help='Ruang lapang untuk atom-atom bergerak di dalam kotak larutan (angstrom).') parser.add_argument('-l','--lapang',type=float, default=5, help='Ruang lapang untuk atom-atom bergerak di dalam kotak larutan (angstrom).')
parser.add_argument('-gen','--generate_dftbinp',type=str,default='false',help='Apakah ingin mengkonversi ke dalam format koordinat xyz?') parser.add_argument('-gen','--generate_dftbinp',type=str,default='false',help='Apakah ingin mengkonversi ke dalam format koordinat xyz?')
parser.add_argument('-prod','--production',type=str,default='None',help='Jenis production run yang ingin dilakukan. Pilihan: NPT (recommended), NVE, dan NVT.') parser.add_argument('-prod','--production',type=str,default='None',help='Jenis production run yang ingin dilakukan. Pilihan: NPT (recommended), NVE, dan NVT.')
parser.add_argument('-np','--nproc',type=int,default=1, help='Jumlah CPU yang digunakan')
parser.add_argument('-rc','--rcol',type=float,default=0, help='Additional Coulombic radius for PME calculation')
opt=parser.parse_args(sys.argv[1:]) opt=parser.parse_args(sys.argv[1:])
@ -52,7 +54,7 @@ pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
;define = -DFLEXIBLE ;define = -DFLEXIBLE
""" """
nve_mdp = """ nve_mdp = """
define = -DFLEXIBLE ;define = -DFLEXIBLE
integrator = md integrator = md
nsteps = {} ; 1 * 500000 = 50 ps nsteps = {} ; 1 * 500000 = 50 ps
dt = 0.001 ; 0.5 fs dt = 0.001 ; 0.5 fs
@ -89,7 +91,7 @@ gen_vel = yes ; Velocity generation is off
# Input file simulasi menggunakan ensembel kanonik (NVT) dalam GROMACS # Input file simulasi menggunakan ensembel kanonik (NVT) dalam GROMACS
nvt_mdp=""" nvt_mdp="""
define = -DFLEXIBLE ;define = -DFLEXIBLE
integrator = md ; leap-frog integrator integrator = md ; leap-frog integrator
nsteps = {} nsteps = {}
dt = 0.001 ; 1 fs dt = 0.001 ; 1 fs
@ -342,7 +344,7 @@ def chargeparm(mol2file,dftbdat):
print(" {} {} {} {} {} {} {} {} {}".format(serial, symbol, x, y, z, type, resid, resname, charge), file=f) print(" {} {} {} {} {} {} {} {} {}".format(serial, symbol, x, y, z, type, resid, resname, charge), file=f)
for line in footer: for line in footer:
print(line, file=f) print(line, file=f)
def make_solution(terlarut,c_terlarut,pelarut,c_pelarut,N_pelarut,persen_terlarut,persen_pelarut,cation, temperature,pressure,packmol,charge_type,lapang,generate_dftbinp,prod): def make_solution(terlarut,c_terlarut,pelarut,c_pelarut,N_pelarut,persen_terlarut,persen_pelarut,cation, temperature,pressure,packmol,charge_type,lapang,generate_dftbinp,prod,nproc):
if temperature: if temperature:
print (f'Suhu: {temperature:12.4f} K') print (f'Suhu: {temperature:12.4f} K')
@ -560,31 +562,32 @@ quit""",file=fout)
nnpt = opt.nnpt nnpt = opt.nnpt
nprod = opt.nprod nprod = opt.nprod
compress = opt.compress compress = opt.compress
rcoulomb = half_box+opt.rcol
rvdw = half_box
with open('minim.mdp', 'w') as f: with open('minim.mdp', 'w') as f:
print(minim_mdp.format(half_box, half_box), file=f) print(minim_mdp.format(rcoulomb, rvdw), file=f)
with open('nve.mdp', 'w') as f: with open('nve.mdp', 'w') as f:
print(nve_mdp.format(nequil,half_box,half_box), file=f) print(nve_mdp.format(nequil,rcoulomb,rvdw), file=f)
with open('nvt.mdp', 'w') as f: with open('nvt.mdp', 'w') as f:
print(nvt_mdp.format(nequil,half_box, half_box,temperature), file=f) print(nvt_mdp.format(nequil,rcoulomb, rvdw,temperature), file=f)
with open('npt.mdp', 'w') as f: with open('npt.mdp', 'w') as f:
print(npt_mdp.format(nnpt,half_box, half_box,temperature,pressure,compress), file=f) print(npt_mdp.format(nnpt,rcoulomb, rvdw,temperature,pressure,compress), file=f)
os.system("cp system.amb2gmx/system_GMX.* .") os.system("cp system.amb2gmx/system_GMX.* .")
gmxscript.grompp(f="minim.mdp", c="system_box.pdb", o="mini.tpr", p="system_GMX.top", maxwarn=2) gmxscript.grompp(f="minim.mdp", c="system_box.pdb", o="mini.tpr", p="system_GMX.top", maxwarn=2)
gmxscript.mdrun(deffnm="mini",ntmpi=1) gmxscript.mdrun(deffnm="mini",ntmpi='{}'.format(opt.nproc))
gmxscript.select(f="mini.trr", s="mini.tpr", on="mini", select="System") gmxscript.select(f="mini.trr", s="mini.tpr", on="mini", select="System")
gmxscript.grompp(f="nve.mdp", c="mini.gro", p="system_GMX.top", o="nve.tpr",maxwarn=2) gmxscript.grompp(f="nve.mdp", c="mini.gro", p="system_GMX.top", o="nve.tpr",maxwarn=2)
gmxscript.mdrun(deffnm="nve", v=True, ntmpi=1) gmxscript.mdrun(deffnm="nve", v=True, ntmpi='{}'.format(opt.nproc))
gmxscript.grompp(f="nvt.mdp", c="nve.gro", p="system_GMX.top", o="nvt.tpr",maxwarn=2) gmxscript.grompp(f="nvt.mdp", c="nve.gro", p="system_GMX.top", o="nvt.tpr",maxwarn=2)
gmxscript.mdrun(deffnm="nvt", v=True, ntmpi=1) gmxscript.mdrun(deffnm="nvt", v=True, ntmpi='{}'.format(opt.nproc))
gmxscript.grompp(f="npt.mdp", c="nvt.gro", p="system_GMX.top", t="nvt.cpt",o="npt.tpr",maxwarn=2) gmxscript.grompp(f="npt.mdp", c="nvt.gro", p="system_GMX.top", t="nvt.cpt",o="npt.tpr",maxwarn=2)
gmxscript.mdrun(deffnm="npt", v=True, ntmpi=1) gmxscript.mdrun(deffnm="npt", v=True, ntmpi='{}'.format(opt.nproc))
if prod == 'npt': if prod == 'npt':
with open('nptp.mdp', 'w') as f: with open('nptp.mdp', 'w') as f:
print(nptp_mdp.format(nprod,opt.dt/2000,half_box,half_box,temperature,compress,pressure), file=f) print(nptp_mdp.format(nprod,opt.dt/2000,rcoulomb,rvdw,temperature,compress,pressure), file=f)
gmxscript.grompp(f="nptp.mdp", c="npt.gro", p="system_GMX.top", o="nptp.tpr",maxwarn=2) gmxscript.grompp(f="nptp.mdp", c="npt.gro", p="system_GMX.top", o="nptp.tpr",maxwarn=2)
gmxscript.mdrun(deffnm="nptp", v=True, ntmpi=1) gmxscript.mdrun(deffnm="nptp", v=True, ntmpi='{}'.format(opt.nproc))
gmxscript.trjconv(f="nptp.trr", s="nptp.tpr", n="mini.ndx", o="finalsystem.pdb") gmxscript.trjconv(f="nptp.trr", s="nptp.tpr", n="mini.ndx", o="finalsystem.pdb")
print("Melakukan perhitungan MSD untuk pelarut") print("Melakukan perhitungan MSD untuk pelarut")
os.system("""gmx select -f nptp.gro -s nptp.tpr -on SLV.ndx -select "(resname SLV)" """) os.system("""gmx select -f nptp.gro -s nptp.tpr -on SLV.ndx -select "(resname SLV)" """)
@ -596,9 +599,9 @@ quit""",file=fout)
if prod == 'nvt': if prod == 'nvt':
with open('nvtp.mdp', 'w') as f: with open('nvtp.mdp', 'w') as f:
print(nvtp_mdp.format(nprod,opt.dt/2000,half_box,half_box,temperature), file=f) print(nvtp_mdp.format(nprod,opt.dt/2000,rcoulomb,rvdw,temperature), file=f)
gmxscript.grompp(f="nvtp.mdp", c="npt.gro", p="system_GMX.top", o="nvtp.tpr",maxwarn=2) gmxscript.grompp(f="nvtp.mdp", c="npt.gro", p="system_GMX.top", o="nvtp.tpr",maxwarn=2)
gmxscript.mdrun(deffnm="nvtp", v=True, ntmpi=1) gmxscript.mdrun(deffnm="nvtp", v=True, ntmpi='{}'.format(opt.nproc))
gmxscript.trjconv(f="nvtp.trr", s="nvtp.tpr", n="mini.ndx", o="finalsystem.pdb") gmxscript.trjconv(f="nvtp.trr", s="nvtp.tpr", n="mini.ndx", o="finalsystem.pdb")
print("Melakukan perhitungan MSD untuk pelarut") print("Melakukan perhitungan MSD untuk pelarut")
os.system("""gmx select -f nvtp.gro -s nvtp.tpr -on SLV.ndx -select "(resname SLV)" """) os.system("""gmx select -f nvtp.gro -s nvtp.tpr -on SLV.ndx -select "(resname SLV)" """)
@ -609,9 +612,9 @@ quit""",file=fout)
os.system("gmx msd -f nvtp.trr -s nvtp.tpr -n {}.ndx -o msd_{}.xvg".format((i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper())) os.system("gmx msd -f nvtp.trr -s nvtp.tpr -n {}.ndx -o msd_{}.xvg".format((i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper()))
if prod == 'nve': if prod == 'nve':
with open('nvep.mdp', 'w') as f: with open('nvep.mdp', 'w') as f:
print(nvep_mdp.format(nprod,opt.dt/2000,half_box,half_box), file=f) print(nvep_mdp.format(nprod,opt.dt/2000,rcoulomb,rvdw), file=f)
gmxscript.grompp(f="nvep.mdp", c="npt.gro", p="system_GMX.top", o="nvep.tpr",maxwarn=2) gmxscript.grompp(f="nvep.mdp", c="npt.gro", p="system_GMX.top", o="nvep.tpr",maxwarn=2)
gmxscript.mdrun(deffnm="nvep", v=True, ntmpi=1) gmxscript.mdrun(deffnm="nvep", v=True, ntmpi='{}'.format(opt.nproc))
gmxscript.trjconv(f="nvep.trr", s="nvep.tpr", n="mini.ndx", o="finalsystem.pdb") gmxscript.trjconv(f="nvep.trr", s="nvep.tpr", n="mini.ndx", o="finalsystem.pdb")
print("Melakukan perhitungan MSD untuk pelarut") print("Melakukan perhitungan MSD untuk pelarut")
os.system("""gmx select -f nvep.gro -s nvep.tpr -on SLV.ndx -select "(resname SLV)" """) os.system("""gmx select -f nvep.gro -s nvep.tpr -on SLV.ndx -select "(resname SLV)" """)
@ -648,4 +651,4 @@ quit""",file=fout)
shutil.rmtree('SistemLarutan', ignore_errors=True) shutil.rmtree('SistemLarutan', ignore_errors=True)
cmmde_solution() cmmde_solution()
# Eksekusi simulasi # Eksekusi simulasi
make_solution(opt.terlarut,opt.c_terlarut,opt.pelarut,opt.c_pelarut,opt.NumPelarut,opt.persen_terlarut,opt.persen_pelarut,opt.cation,opt.temperature,opt.pressure,opt.packmol,opt.charge_type,opt.lapang,opt.generate_dftbinp,opt.production) make_solution(opt.terlarut,opt.c_terlarut,opt.pelarut,opt.c_pelarut,opt.NumPelarut,opt.persen_terlarut,opt.persen_pelarut,opt.cation,opt.temperature,opt.pressure,opt.packmol,opt.charge_type,opt.lapang,opt.generate_dftbinp,opt.production,opt.nproc)

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