#!/usr/bin/env python3
import subprocess
import os
import shutil
import gmxscript
from scipy . constants import N_A
import argparse
import sys
import time
from cmmde_mass import mass
parser = argparse . ArgumentParser ( description = ' SPE Solution Program ' )
parser . add_argument ( ' -mt ' , ' --terlarut ' , type = str , help = ' Nama file molekul terlarut dalam format .xyz (ditulis tanpa ekstensi). ' )
parser . add_argument ( ' -ctype ' , ' --charge_type ' , type = str , default = ' gas ' , help = ' Tipe muatan yang digunakan untuk parameterisasi muatan. Pilihan: gas, bcc, dftb ' )
parser . add_argument ( ' -ct ' , ' --c_terlarut ' , type = str , help = ' Muatan bersih molekul terlarut. Jika terlarut lebih dari satu buah, pisahkan dengan koma ' )
parser . add_argument ( ' -pt ' , ' --persen_terlarut ' , type = str , help = ' Fraksi massa terlarut dalam persen. Jika pelarut lebih dari satu buah, pisahkan menggunakan koma. ' )
parser . add_argument ( ' -pp ' , ' --persen_pelarut ' , type = float , help = ' Fraksi massa pelarut dalam persen. ' )
parser . add_argument ( ' -mp ' , ' --pelarut ' , type = str , help = ' Nama file molekul pelarut dalam format .xyz (ditulis tanpa ekstensi). ' )
parser . add_argument ( ' -cp ' , ' --c_pelarut ' , type = int , help = ' Muatan bersih molekul pelarut ' , default = 0 )
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 dalam sistem elektrolit baterai. ' )
parser . add_argument ( ' -p ' , ' --pressure ' , default = 1.0 , type = float , help = ' Tekanan dalam satuan bar ' )
parser . add_argument ( ' -t ' , ' --temperature ' , default = 298.15 , type = float , help = ' Suhu yang digunakan dalam simulasi. ' )
parser . add_argument ( ' -nequil ' , ' --nequil ' , type = int , default = 50000 , help = ' Jumlah step pada saat ekuilibrasi. ' )
parser . add_argument ( ' -nnpt ' , ' --nnpt ' , type = int , default = 50000 , help = ' Jumlah step pada saat ekuilibrasi NPT. ' )
parser . add_argument ( ' -nprod ' , ' --nprod ' , type = int , default = 400000 , help = ' Jumlah step pada saat production. ' )
parser . add_argument ( ' -dt ' , ' --dt ' , type = float , default = 1 , help = ' Step simulasi dinamika molekul yang dilakukan. ' )
parser . add_argument ( ' -comp ' , ' --compress ' , type = float , default = 4.5e-6 , help = ' Nilai kompresibilitas. Default=4.5e-6. ' )
parser . add_argument ( ' --packmol ' , type = str , default = ' /Users/adit/opt/packmol/packmol ' )
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 ( ' -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 : ] )
# Input file minimisasi energi dalam GROMACS
minim_mdp = """
integrator = cg ; Algorithm ( steep or cg )
emtol = 1 ; Stop minimization when the maximum force < 1 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 = { } ; Short - range electrostatic cut - off
rvdw = { } ; Short - range Van der Waals cut - off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
; define = - DFLEXIBLE
"""
nve_mdp = """
; define = - DFLEXIBLE
integrator = md
nsteps = { } ; 1 * 500000 = 50 ps
dt = 0.001 ; 0.5 fs
nstxout = 100 ; save coordinates every 1.0 ps
nstenergy = 100 ; save energies every 1.0 ps
nstlog = 100 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; 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
; Nonbonded settings
cutoff - scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs , largely irrelevant with Verlet
rcoulomb = { } ; short - range electrostatic cutoff ( in nm )
rvdw = { } ; short - range van der Waals cutoff ( in nm )
DispCorr = EnerPres ; account for cut - off vdW scheme
; 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 off
tcoupl = no ; no temperature coupling in NVE
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVE
; Periodic boundary conditions
pbc = xyz ; 3 - D PBC
; Velocity generation
gen_vel = yes ; Velocity generation is off
"""
# Input file simulasi menggunakan ensembel kanonik (NVT) dalam GROMACS
nvt_mdp = """
; define = - DFLEXIBLE
integrator = md ; leap - frog integrator
nsteps = { }
dt = 0.001 ; 1 fs
nstxout = 100 ; save coordinates every 1.0 ps
; nstenergy = 100 ; save energies every 1.0 ps
; nstlog = 100 ; 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
; Nonbonded settings
cutoff - scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs , largely irrelevant with Verlet
rcoulomb = { } ; short - range electrostatic cutoff ( in nm )
rvdw = { } ; short - range van der Waals cutoff ( in nm )
DispCorr = EnerPres ; account for cut - off vdW scheme
; 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 = 0.01 ; time constant , in ps
ref_t = { } ; reference temperature , one for each group , in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3 - D PBC
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
"""
# Input file simulasi isoterm-isobarik (NPT) dalam GROMACS. Harapannya, setelah dilakukan NPT, akan diperoleh sistem dengan massa jenis yang optimal.
npt_mdp = """
title = NPT equilibration
; Run parameters
integrator = md ; leap - frog integrator
nsteps = { }
dt = 0.001 ; 1 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 = 6 ; 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 = { } ; short - range electrostatic cutoff ( in nm )
rvdw = { } ; 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 = { } ; 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 ; time constant , in ps
ref_p = { } ; reference pressure , in bar
compressibility = { } ; 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
"""
nptp_mdp = """
title = NPT Production
; Run parameters
integrator = md ; leap - frog integrator
nsteps = { } ;
dt = { } ; in ps
; 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 ; if no = > first dynamics run
; Neighborsearching
cutoff - scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs , largely irrelevant with Verlet scheme
rcoulomb = { } ; short - range electrostatic cutoff ( in nm )
rvdw = { } ; 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 off
tcoupl = V - rescale ; modified Berendsen thermostat
tc - grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant , in ps
ref_t = { } ; 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 = 10 ; time constant , in ps
compressibility = { } ; isothermal compressibility of water , bar ^ - 1
ref_p = { } ; reference pressure , in bar
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
"""
nvtp_mdp = """
title = NVT Production
; Run parameters
integrator = md ; leap - frog integrator
nsteps = { } ;
dt = { } ; in ps
; 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 ; if no = > first dynamics run
; Neighborsearching
cutoff - scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs , largely irrelevant with Verlet scheme
rcoulomb = { } ; short - range electrostatic cutoff ( in nm )
rvdw = { } ; 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 off
tcoupl = V - rescale ; modified Berendsen thermostat
tc - grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant , in ps
ref_t = { } ; reference temperature , one for each group , in K
; Pressure coupling is off in NVT simulation
pcoupl = no ; Pressure coupling on in NPT
; 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
"""
nvep_mdp = """
title = NVE Production
; Run parameters
integrator = md ; leap - frog integrator
nsteps = { } ;
dt = { } ; in ps
; 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 ; if no = > first dynamics run
; Neighborsearching
cutoff - scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs , largely irrelevant with Verlet scheme
rcoulomb = { } ; short - range electrostatic cutoff ( in nm )
rvdw = { } ; 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 off
tcoupl = no ; modified Berendsen thermostat
; Pressure coupling is off in NVE simulation
pcoupl = no ; Pressure coupling on in NPT
; 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
"""
def chargeparm ( mol2file , dftbdat ) :
header = [ ]
footer = [ ]
serial = [ ]
symbol = [ ]
x = [ ]
y = [ ]
z = [ ]
type = [ ]
resid = [ ]
resname = [ ]
charge = [ ]
with open ( mol2file , ' r ' ) as f :
for i in range ( 1 , 9 ) :
header . append ( next ( f ) . strip ( ) )
for line in range ( 1 , int ( header [ 2 ] . split ( ) [ 0 ] ) + 1 ) :
arr = next ( f ) . split ( )
serial . append ( arr [ 0 ] )
symbol . append ( arr [ 1 ] )
x . append ( arr [ 2 ] )
y . append ( arr [ 3 ] )
z . append ( arr [ 4 ] )
type . append ( arr [ 5 ] )
resid . append ( arr [ 6 ] )
resname . append ( arr [ 7 ] )
for line in f :
footer . append ( line . strip ( ) )
with open ( dftbdat , ' r ' ) as f :
for line in f :
if ' MULLIKEN ' in line :
next ( f )
for i in range ( 1 , int ( header [ 2 ] . split ( ) [ 0 ] ) + 1 ) :
arr = next ( f ) . split ( )
charge . append ( arr [ 2 ] )
fname = mol2file . split ( " . " ) [ 0 ]
with open ( " {} _mod.mol2 " . format ( fname ) , ' w ' ) as f :
for line in header [ 0 : 4 ] :
print ( line , file = f )
print ( " DFTBCharge " , file = f )
print ( """
@ < TRIPOS > ATOM """ ,file=f)
for serial , symbol , x , y , z , type , resid , resname , charge in zip ( serial , symbol , x , y , z , type , resid , resname , charge ) :
print ( " {} {} {} {} {} {} {} {} {} " . format ( serial , symbol , x , y , z , type , resid , resname , charge ) , file = f )
for line in footer :
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 , nproc ) :
if temperature :
print ( f ' Suhu: { temperature : 12.4f } K ' )
# Penyiapan box molekul
terlarut = terlarut . split ( " , " )
c_terlarut = c_terlarut . split ( " , " )
c_terlarut = dict ( zip ( terlarut , c_terlarut ) )
for i in terlarut :
os . chdir ( ' {} ' . format ( i ) )
if charge_type == ' dftb ' :
os . system ( " obabel cmmd.xyz -O {} .pdb " . format ( i ) )
else :
os . system ( " rm geom.xyz " )
os . system ( " rm cmmd_trj.xyz " )
os . system ( " obabel *.xyz -O {} .pdb " . format ( i ) )
with open ( ' {} .pdb ' . format ( i ) , ' r ' ) as f :
fdata = f . read ( )
fdata = fdata . replace ( ' UNL ' , ' {} ' . format ( ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) ) )
fdata = fdata . replace ( ' CONECT ' , ' #CONECT ' )
with open ( ' {} .pdb ' . format ( i ) , ' w ' ) as f :
f . write ( fdata )
if opt . charge_type == ' dftb ' :
charge_type = ' gas '
os . system ( " antechamber -j 5 -at gaff -dr no -i {} .pdb -fi pdb -o {} .mol2 -fo mol2 -c {} -s 2 -nc {} " . format ( i , i , charge_type , float ( c_terlarut [ i ] ) ) )
chargeparm ( " {} .mol2 " . format ( i ) , " dftb.dat " )
else :
os . system ( " antechamber -j 5 -at gaff -dr no -i {} .pdb -fi pdb -o {} .mol2 -fo mol2 -c {} -s 2 -nc {} " . format ( i , i , charge_type , float ( c_terlarut [ i ] ) ) )
os . system ( " cp {} .mol2 {} _mod.mol2 " . format ( i , i ) )
os . system ( " parmchk2 -i {} _mod.mol2 -f mol2 -o {} .frcmod " . format ( i , i ) )
with open ( " tleap.in " , ' w ' ) as fout :
print ( """
source leaprc . gaff
{ } = loadmol2 { } _mod . mol2
loadamberparams { } . frcmod
check { }
saveoff { } { } . lib
saveamberparm { } { } . parmtop { } . inpcrd
savepdb { } { } _gaff . pdb
quit
""" .format((i[0]+i[1]+i[-1]).upper(), i, i, (i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper(),(i[0]+i[1]+i[-1]).upper()), file=fout)
os . system ( " tleap -f tleap.in " )
os . chdir ( ' ../ ' )
os . chdir ( ' {} ' . format ( pelarut ) )
# Penyiapan molekul pelarut menggunakan GAFF
# Memanggil antechamber untuk membuatkan file mol2 yang mengandung informasi muatan bersih atom
if charge_type == ' dftb ' :
os . system ( " obabel cmmd.xyz -O {} .pdb " . format ( pelarut ) )
else :
os . system ( " rm geom.xyz " )
os . system ( " rm cmmd_trj.xyz " )
os . system ( " obabel *.xyz -O {} .pdb " . format ( pelarut ) )
with open ( ' {} .pdb ' . format ( pelarut ) , ' r ' ) as f :
fdata = f . read ( )
fdata = fdata . replace ( ' UNL ' , ' SLV ' )
fdata = fdata . replace ( ' HOH ' , ' SLV ' )
fdata = fdata . replace ( ' CONECT ' , ' #CONECT ' )
with open ( ' {} .pdb ' . format ( pelarut ) , ' w ' ) as f :
f . write ( fdata )
if opt . charge_type == ' dftb ' :
charge_type = ' gas '
os . system ( " antechamber -j 5 -at gaff -dr no -i {} .pdb -fi pdb -o {} .mol2 -fo mol2 -c {} -s 2 -nc {} " . format ( pelarut , pelarut , charge_type , c_pelarut ) )
chargeparm ( " {} .mol2 " . format ( pelarut ) , " dftb.dat " )
# Mengidentifikasi parameter yang tidak terdefinisikan dalam GAFF
else :
os . system ( " antechamber -j 5 -at gaff -dr no -i {} .pdb -fi pdb -o {} .mol2 -fo mol2 -c {} -s 2 -nc {} " . format ( pelarut , pelarut , charge_type , c_pelarut ) )
os . system ( " cp {} .mol2 {} _mod.mol2 " . format ( pelarut , pelarut ) )
os . system ( " parmchk2 -i {} _mod.mol2 -f mol2 -o {} .frcmod " . format ( pelarut , pelarut ) )
with open ( " tleap.in " , ' w ' ) as fout :
print ( """
source leaprc . gaff
SLV = loadmol2 { } _mod . mol2
loadamberparams { } . frcmod
check SLV
saveoff SLV { } . lib
saveamberparm SLV { } . parmtop { } . inpcrd
savepdb SLV { } _gaff . pdb
quit
""" .format(pelarut,pelarut,pelarut,pelarut,pelarut,pelarut), file=fout)
os . system ( " tleap -f tleap.in " )
if cation != ' none ' :
os . system ( " mkdir ../ {} " . format ( cation ) )
os . chdir ( ' ../ {} ' . format ( cation ) )
with open ( ' {} .mol2 ' . format ( cation ) , ' w ' ) as f :
print ( """ @<TRIPOS>MOLECULE
ION
1 0 0 0 0
SMALL
GASTEIGER
@ < TRIPOS > ATOM
1 { } + 0.0000 0.0000 0.0000 { } + 1 ion 1.0000
@ < TRIPOS > BOND
""" .format(cation,cation),file=f)
# Penyiapan box
os . chdir ( ' ../ ' )
with open ( " {} /cmmd.xyz " . format ( pelarut ) , ' r ' ) as f :
elements = [ ]
Mr_pelarut = 0
next ( f )
next ( f )
for line in f :
arr = line . split ( )
elements . append ( arr [ 0 ] )
for ele in elements :
Mr_pelarut + = float ( mass ( ele ) )
Mr_terlarut = [ ]
for i in terlarut :
ele_terlarut = [ ]
Mr_t = 0
with open ( " {} /cmmd.xyz " . format ( i ) , ' r ' ) as f :
next ( f )
next ( f )
for line in f :
arr = line . split ( )
ele_terlarut . append ( arr [ 0 ] )
for ele in ele_terlarut :
Mr_t + = float ( mass ( ele ) )
Mr_terlarut . append ( Mr_t )
Mr_terlarut = dict ( zip ( terlarut , Mr_terlarut ) )
m_pelarut = N_pelarut * ( Mr_pelarut / N_A ) # dalam g
m_larutan = m_pelarut / persen_pelarut * 100
persen_terlarut = persen_terlarut . split ( " , " )
persen_terlarut = dict ( zip ( terlarut , persen_terlarut ) )
N_terlarut = [ ]
for i in terlarut :
N = round ( ( float ( persen_terlarut [ i ] ) / 100 ) * m_larutan / Mr_terlarut [ i ] * N_A )
N_terlarut . append ( N )
N_terlarut = dict ( zip ( terlarut , N_terlarut ) )
V_box = m_larutan # Dalam satuan cm3
# Panjang rusuk kubus dalam satuan cm:
box_size = V_box * * ( 1 / 3 )
# Panjang rusuk kubus dalam satuan Angstroem:
cmToAng = 1e8
box_size = box_size * cmToAng + lapang
# Hentikan perhitungan jika ukuran kubus terlalu kecil
half_box = min ( 1.0 , box_size / 20.0 - 0.1 )
print ( half_box )
def cmmde_solution ( ) :
cwd = os . path . abspath ( os . curdir )
print ( ' Membuat sistem larutan menggunakan PACKMOL ' )
os . makedirs ( ' SistemLarutan ' , exist_ok = True )
os . chdir ( ' SistemLarutan ' )
with open ( ' packmol.inp ' , ' w ' ) as fout :
print ( """ tolerance 2.5
filetype pdb
output system_init . pdb
structure . . / { } / { } _gaff . pdb
number { }
inside cube - { } - { } - { } { }
resnumbers 3
end structure """ .format(pelarut, pelarut, N_pelarut, box_size/2.0, box_size/2.0, box_size/2.0, box_size), file=fout)
for i in terlarut :
print ( """ structure ../ {} / {} _gaff.pdb
number { }
inside cube - { } - { } - { } { }
resnumbers 3
end structure """ .format(i,(i[0]+i[1]+i[-1]).upper(),N_terlarut[i],box_size/2.0, box_size/2.0, box_size/2.0, box_size), file=fout)
print ( ' = ' * 80 )
with open ( ' tleap.in ' , ' w ' ) as fout :
print ( """ source leaprc.gaff
loadamberparams / Users / adit / opt / amber22 / dat / leap / parm / frcmod . ionslm_iod_opc3 """ , file=fout)
for i in terlarut :
print ( """ loadoff ../ {} / {} .lib
loadamberparams . . / { } / { } . frcmod """ .format(i,(i[0]+i[1]+i[-1]).upper(),i,i),file=fout)
print ( """ loadoff ../ {} / {} .lib
loadamberparams . . / { } / { } . frcmod
SYSTEM = loadpdb system_init . pdb """ .format(pelarut,pelarut,pelarut,pelarut),file=fout)
if cation != ' none ' :
print ( """ ION = loadmol2 ../ {} / {} .mol2
addions SYSTEM ION 0 """ .format(cation,cation),file=fout)
print ( """ list
saveamberparm SYSTEM system . prmtop system . inpcrd
savepdb SYSTEM system . pdb
quit """ ,file=fout)
with open ( ' packmol.inp ' , ' r ' ) as f :
print ( f . read ( ) )
print ( ' = ' * 80 )
os . system ( " {} < packmol.inp " . format ( packmol ) )
os . system ( " tleap -f tleap.in " )
os . system ( " acpype -p system.prmtop -x system.inpcrd " )
gmxscript . editconf (
f = " system.pdb " ,
box = [ box_size / 10.0 , box_size / 10.0 , box_size / 10.0 ] ,
bt = " cubic " ,
o = " system_box.pdb "
)
# Menuliskan semua input file yang dibutuhkan, meliputi simulasi NVE, NVT, dan NPT
nequil = opt . nequil
nnpt = opt . nnpt
nprod = opt . nprod
compress = opt . compress
rcoulomb = half_box + opt . rcol
rvdw = half_box
with open ( ' minim.mdp ' , ' w ' ) as f :
print ( minim_mdp . format ( rcoulomb , rvdw ) , file = f )
with open ( ' nve.mdp ' , ' w ' ) as f :
print ( nve_mdp . format ( nequil , rcoulomb , rvdw ) , file = f )
with open ( ' nvt.mdp ' , ' w ' ) as f :
print ( nvt_mdp . format ( nequil , rcoulomb , rvdw , temperature ) , file = f )
with open ( ' npt.mdp ' , ' w ' ) as f :
print ( npt_mdp . format ( nnpt , rcoulomb , rvdw , temperature , pressure , compress ) , file = f )
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 . mdrun ( deffnm = " mini " , ntmpi = ' {} ' . format ( opt . nproc ) )
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 . 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 . 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 . mdrun ( deffnm = " npt " , v = True , ntmpi = ' {} ' . format ( opt . nproc ) )
if prod == ' npt ' :
with open ( ' nptp.mdp ' , ' w ' ) as 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 . mdrun ( deffnm = " nptp " , v = True , ntmpi = ' {} ' . format ( opt . nproc ) )
gmxscript . trjconv ( f = " nptp.trr " , s = " nptp.tpr " , n = " mini.ndx " , o = " finalsystem.pdb " )
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 msd -f nptp.trr -s nptp.tpr -n SLV.ndx -o msd_SLV.xvg " )
print ( " Melakukan perhitungan MSD untuk terlarut, masukkan masing-masing terlarut " )
for i in terlarut :
os . system ( """ gmx select -f nptp.gro -s nptp.tpr -on {} .ndx -select " (resname {} ) " """ . format ( ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) , ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) ) )
os . system ( " gmx msd -f nptp.trr -s nptp.tpr -n {} .ndx -o msd_ {} .xvg " . format ( ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) , ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) ) )
if prod == ' nvt ' :
with open ( ' nvtp.mdp ' , ' w ' ) as 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 . mdrun ( deffnm = " nvtp " , v = True , ntmpi = ' {} ' . format ( opt . nproc ) )
gmxscript . trjconv ( f = " nvtp.trr " , s = " nvtp.tpr " , n = " mini.ndx " , o = " finalsystem.pdb " )
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 msd -f nvtp.trr -s nvtp.tpr -n SLV.ndx -o msd_SLV.xvg " )
print ( " Melakukan perhitungan MSD untuk terlarut, masukkan masing-masing terlarut " )
for i in terlarut :
os . system ( """ gmx select -f nvtp.gro -s nvtp.tpr -on {} .ndx -select " (resname {} ) " """ . 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 ' :
with open ( ' nvep.mdp ' , ' w ' ) as 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 . mdrun ( deffnm = " nvep " , v = True , ntmpi = ' {} ' . format ( opt . nproc ) )
gmxscript . trjconv ( f = " nvep.trr " , s = " nvep.tpr " , n = " mini.ndx " , o = " finalsystem.pdb " )
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 msd -f nvep.trr -s nvep.tpr -n SLV.ndx -o msd_SLV.xvg " )
print ( " Melakukan perhitungan MSD untuk terlarut, masukkan masing-masing terlarut " )
for i in terlarut :
os . system ( """ gmx select -f nvep.gro -s nvep.tpr -on {} .ndx -select " (resname {} ) " """ . format ( ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) , ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) ) )
os . system ( " gmx msd -f nvep.trr -s nvep.tpr -n {} .ndx -o msd_ {} .xvg " . format ( ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) , ( i [ 0 ] + i [ 1 ] + i [ - 1 ] ) . upper ( ) ) )
if generate_dftbinp != ' false ' :
os . system ( " obabel finalsystem.pdb -O finalsystem.xyz " )
with open ( ' finalsystem.xyz ' , ' r ' ) as f :
fdata = f . read ( )
fdata = fdata . replace ( ' * ' , ' {} ' . format ( opt . cation ) )
with open ( ' finalsystem.pdb ' , ' r ' ) as f :
tv1 = 0
tv2 = 0
tv3 = 0
for line in f :
if ' CRYST ' in line :
arr = line . split ( )
tv1 + = float ( arr [ 1 ] )
tv2 + = float ( arr [ 2 ] )
tv3 + = float ( arr [ 3 ] )
break
with open ( ' finalsystem.xyz ' . format ( terlarut ) , ' w ' ) as fout :
fout . write ( fdata )
print ( " TV {} 0.00 0.00 " . format ( tv1 ) , file = fout )
print ( " TV 0.00 {} 0.00 " . format ( tv2 ) , file = fout )
print ( " TV 0.00 0.00 {} " . format ( tv3 ) , file = fout )
os . chdir ( cwd )
shutil . rmtree ( ' SistemLarutan ' , ignore_errors = True )
cmmde_solution ( )
# 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 , opt . nproc )
