"""
This file is part of the AdaptiveMasterMSM package.
"""
import os
import subprocess
import shlex
# AdaptiveMasterMSM
from ..system import system_lib
[docs]def check_gmx():
"""
Checks the available Gromacs version.
"""
output = subprocess.check_output("which gmx", shell=True)
print ("%s"%output)
[docs]class System(object):
"""
Create files to be able to run GROMACS
"""
def __init__(self, pdb, forcefield=None, water=None,\
topology=None, constraints=None):
"""
Parameters
----------
pdb : str
Path to the PDB or GRO file to start setup
forcefield : str
Name of force field in Gromacs format (e.g. amber96)
water : str
Water model for GROMACS (e.g. tip3p)
topology : str
Path to topology TOP file
constraints : str
Parameter for the minimization MDP file (e.g. h-bonds)
"""
# Read user-defined parameters
self.pdb = pdb
if forcefield is not None:
self.ff = forcefield
self.wat = water
elif topology is not None:
self.top = topology
self.cons = constraints
[docs] def gen_top(self, gro='conf.gro', top='topol.top'):
"""
Generates topology from structure file.
"""
pdb = self.pdb
self.gro = gro
ff = self.ff
wat = self.wat
self.top = top
cmd = "gmx pdb2gmx -f %s -o %s -p %s -ff %s -water %s"%\
(pdb, gro, top, ff, wat)
print (cmd)
os.system(cmd)
[docs] def build_box(self, out='conf_edit.gro', d=1.0):
"""
Generates the box for the system
Parameters
----------
d : float
Distance between solute and box sides
"""
if self.gro is None: self.gro = 'conf.gro'
gro = self.gro
cmd = 'gmx editconf -f %s -o %s -c -d %f -bt cubic' %(gro, out, d)
print (cmd)
os.system(cmd)
self.gro = out
[docs] def solvate(self, inp='conf_edit.gro', out='conf_solv.gro', top='topol.top'):
"""
Solvates the system using gmx solvate
"""
# Choose a water topology file
water_dict = {'tip3p' : 'spc216.gro'}
if self.wat in water_dict.keys():
water_topol = water_dict[self.wat]
else:
print ("Could not find a topology in 'w_top_dict' for water: %s" % self.wat)
raise Exception("Invalid water model for GROMACS.")
cmd = 'gmx solvate -cp %s -cs %s -p %s -o %s' %\
(inp, water_topol, top, out)
print (cmd)
os.system(cmd)
self.gro = out
[docs] def ionize(self, neutral=True, conc=None, inp='conf_solv.gro',\
out='conf_solv_ions.gro', top='topol.top', tpr='ions.tpr'):
"""
Adds ions for electroneutrality and / or target concentration.
Parameters
----------
neutral : bool
Whether we neutralize the simulation box.
conc : float
The target salt concentration in M.
"""
# Format the water string
if not conc:
ion_str = '-neutral'
else:
ion_str = '-conc %g'%conc
# Generate the tpr file required for gmx genion
self.mdpfile = system_lib.write_minimization_mdp(self.cons)
cmd = "gmx grompp -f %s -c %s -p %s -o %s"%(self.mdpfile, inp, top, tpr)
print(cmd)
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
output, error = p.communicate()
# Run genion
cmd = "gmx genion -s %s -o %s -p %s %s"%(tpr, out, top, ion_str)
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
output, error = p.communicate()
print(cmd)
self.gro = out
# def minimize(self, inp='conf_solv_ions.gro', top='topol.top', out='minimization'):
# """
# Runs minimization invoking the Launcher class
#
# """
# self.mdpfile = system_lib.write_minimization_mdp(self.cons)
# cmd = 'gmx grompp -f %s -c %s -p %s -o %s'% (self.mdpfile, inp, top, out)
# print(cmd)
# p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
# output, error = p.communicate()
#
# cmd = 'gmx mdrun -v -s %s.tpr -deffnm %s'%(out, out)
# p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
# output, error = p.communicate()
# self.gro = out + ".gro"
#
# def nvt(self, mdp='nvt.mdp', gro='minimization.gro',\
# top='topol.top', tpr='nvt.tpr', out='nvt'):
#
# cmd = 'gmx grompp -f %s -c %s -r %s -p %s -o %s; gmx mdrun -v -s %s -deffnm %s'\
# % (mdp, gro, gro, top, tpr, tpr, out)
# print(cmd)
# p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
# output, error = p.communicate()
# return output, error
#
# def npt(self, mdp='npt.mdp', gro='nvt.gro', chk='nvt.cpt',\
# top='topol.top', tpr='npt.tpr', out='npt'):
#
# cmd = 'gmx grompp -f %s -c %s -r %s -t %s -p %s -o %s; gmx mdrun -v -s %s -deffnm %s'\
# % (mdp, gro, gro, chk, top, tpr, tpr, out)
# print(cmd)
# p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
# output, error = p.communicate()
# return output, error
