def run(self):
""" runs a gromacs-mdrun with the
current atom-configuration """
# clean up gromacs backups
if self.clean:
do_clean('#*')
subcmd = 'mdrun'
command = [subcmd]
if self.do_qmmm:
command += [
'-s', self.label + '.tpr', '-o', self.label + '.trr', '-e',
self.label + '.edr', '-g', self.label + '.log', '-rerun',
self.label + '.g96',
self.params_runs.get('extra_mdrun_parameters',
''), '> QMMM.log 2>&1'
]
command = ' '.join(command)
self._execute_gromacs(command)
else:
command += [
'-s', self.label + '.tpr', '-o', self.label + '.trr', '-e',
self.label + '.edr', '-g', self.label + '.log', '-c',
self.label + '.g96',
self.params_runs.get('extra_mdrun_parameters',
''), '> MM.log 2>&1'
]
command = ' '.join(command)
self._execute_gromacs(command)
atoms = read_gromos(self.label + '.g96')
self.atoms = atoms.copy()
def generate_topology_and_g96file(self):
""" from coordinates (self.label.+'pdb')
and gromacs run input file (self.label + '.mdp)
generate topology (self.label+'top')
and structure file in .g96 format (self.label + '.g96')
"""
from ase.io.gromos import read_gromos
#generate structure and topology files
# In case of predefinded topology file this is not done
command = 'pdb2gmx' + ' '
os.system(command + \
' -f ' + self.params_runs.get('init_structure') + \
' -o ' + self.label + '.g96' + \
' -p ' + self.label + '.top' + \
' -ff ' + self.params_runs.get('force_field') + \
' -water ' + self.params_runs.get('water') + \
' ' + \
self.params_runs.get('extra_pdb2gmx_parameters') +\
' > /dev/null 2>&1')
# ' > debug.log 2>&1')
# print command + \
# ' -f ' + self.params_runs.get('init_structure') + \
# ' -o ' + self.label+'.g96' + \
# ' -p ' + self.label+'.top' + \
# ' -ff ' + self.params_runs.get('force_field') + \
# ' -water ' + self.params_runs.get('water') + \
# ' ' + self.params_runs.get('extra_pdb2gmx_parameters') +\
# ' > /dev/null 2>&1'
atoms = read_gromos(self.label + '.g96')
self.atoms = atoms.copy()
def run(self):
""" runs a 0-step gromacs-mdrun with the
current atom-configuration """
delnames = glob.glob('#*')
try:
for delname in delnames:
os.remove(delname)
except:
pass
command = self.get_command()
if self.doing_qmmm:
os.system(command \
+ ' -s ' + self.base_filename + '.tpr' \
+ ' -o ' + self.base_filename + '.trr ' \
+ ' -e ' + self.base_filename + '.edr ' \
+ ' -g ' + self.base_filename + '.log -ffout ' \
+ ' -rerun ' + self.structure_file \
+ ' ' + self.extra_mdrun_parameters \
+ ' > mm.log 2>&1')
else:
os.system(command \
+ ' -s ' + self.base_filename + '.tpr' \
+ ' -o ' + self.base_filename + '.trr' \
+ ' -e ' + self.base_filename + '.edr' \
+ ' -g ' + self.base_filename + '.log -ffout ' \
+ ' -c ' + self.structure_file \
+ ' ' + self.extra_mdrun_parameters \
+ ' > MM.log 2>&1')
atoms = read_gromos(self.structure_file)
self.atoms = atoms.copy()
def run(self):
""" runs a gromacs-mdrun with the
current atom-configuration """
from ase.io.gromos import read_gromos
# clean up gromacs backups
if self.clean:
do_clean('#*')
command = 'mdrun'
if self.do_qmmm:
os.system(command \
+ ' -s ' + self.label + '.tpr' \
+ ' -o ' + self.label + '.trr ' \
+ ' -e ' + self.label + '.edr ' \
+ ' -g ' + self.label + '.log -ffout ' \
+ ' -rerun ' + self.label + '.g96 ' \
+ self.params_runs.get('extra_mdrun_parameters') \
+ ' > mm.log 2>&1')
else:
os.system(command \
+ ' -s ' + self.label + '.tpr ' \
+ ' -o ' + self.label + '.trr ' \
+ ' -e ' + self.label + '.edr ' \
+ ' -g ' + self.label + '.log -ffout ' \
+ ' -c ' + self.label + '.g96 ' \
+ self.params_runs.get('extra_mdrun_parameters') \
+ ' > MM.log 2>&1')
atoms = read_gromos(self.label + '.g96')
self.atoms = atoms.copy()
def generate_topology_and_g96file(self):
""" from coordinates (self.label.+'pdb')
and gromacs run input file (self.label + '.mdp)
generate topology (self.label+'top')
and structure file in .g96 format (self.label + '.g96')
"""
from ase.io.gromos import read_gromos
#generate structure and topology files
# In case of predefinded topology file this is not done
command = 'pdb2gmx' + ' '
os.system(command + \
' -f ' + self.params_runs.get('init_structure') + \
' -o ' + self.label + '.g96' + \
' -p ' + self.label + '.top' + \
' -ff ' + self.params_runs.get('force_field') + \
' -water ' + self.params_runs.get('water') + \
' ' + \
self.params_runs.get('extra_pdb2gmx_parameters') +\
' > /dev/null 2>&1')
# ' > debug.log 2>&1')
# print command + \
# ' -f ' + self.params_runs.get('init_structure') + \
# ' -o ' + self.label+'.g96' + \
# ' -p ' + self.label+'.top' + \
# ' -ff ' + self.params_runs.get('force_field') + \
# ' -water ' + self.params_runs.get('water') + \
# ' ' + self.params_runs.get('extra_pdb2gmx_parameters') +\
# ' > /dev/null 2>&1'
atoms = read_gromos(self.label + '.g96')
self.atoms = atoms.copy()
def run(self):
""" runs a gromacs-mdrun with the
current atom-configuration """
from ase.io.gromos import read_gromos
# clean up gromacs backups
if self.clean:
do_clean('#*')
command = 'mdrun'
if self.do_qmmm:
os.system(command \
+ ' -s ' + self.label + '.tpr' \
+ ' -o ' + self.label + '.trr ' \
+ ' -e ' + self.label + '.edr ' \
+ ' -g ' + self.label + '.log -ffout ' \
+ ' -rerun ' + self.label + '.g96 ' \
+ self.params_runs.get('extra_mdrun_parameters') \
+ ' > mm.log 2>&1')
else:
os.system(command \
+ ' -s ' + self.label + '.tpr ' \
+ ' -o ' + self.label + '.trr ' \
+ ' -e ' + self.label + '.edr ' \
+ ' -g ' + self.label + '.log -ffout ' \
+ ' -c ' + self.label + '.g96 ' \
+ self.params_runs.get('extra_mdrun_parameters') \
+ ' > MM.log 2>&1')
atoms = read_gromos(self.label + '.g96')
self.atoms = atoms.copy()
def generate_topology_and_g96file(self):
""" from coordinates (self.label.+'pdb')
and gromacs run input file (self.label + '.mdp)
generate topology (self.label+'top')
and structure file in .g96 format (self.label + '.g96')
"""
#generate structure and topology files
# In case of predefinded topology file this is not done
subcmd = 'pdb2gmx'
command = ' '.join([
subcmd, '-f', self.params_runs['init_structure'], '-o',
self.label + '.g96', '-p', self.label + '.top', '-ff',
self.params_runs['force_field'], '-water',
self.params_runs['water'],
self.params_runs.get('extra_pdb2gmx_parameters', ''),
'> {}.{}.log 2>&1'.format(self.label, subcmd)
])
self._execute_gromacs(command)
atoms = read_gromos(self.label + '.g96')
self.atoms = atoms.copy()
def generate_topology_and_g96file(self):
""" from coordinates (self.structure_file)
and gromacs run input file (' + self.base_filename + '.mdp)
generate topology 'self.topology_filename'
and structure file in .g96 format
"""
import os.path
#generate structure and topology files
# In case of predefinded topology file this is not done
command = self.prefix + 'pdb2gmx' + self.postfix + ' '
os.system(command + \
' -f ' + self.init_structure_file + \
' -o ' + self.structure_file + \
' -p ' + self.topology_filename + \
' -ff ' + self.force_field + \
' -water ' + self.water_model + \
' ' + self.extra_pdb2gmx_parameters +\
' > /dev/null 2>&1')
# ' > debug.log 2>&1')
atoms = read_gromos(self.structure_file)
self.atoms = atoms.copy()
def read_atoms(self):
""" read atoms from file """
self.atoms = read_gromos(self.structure_file)
nsteps = '0',
nstfout = '1',
nstlog = '1',
nstenergy = '1',
nstlist = '1',
ns_type = 'grid',
pbc = 'xyz',
rlist = '1.15',
coulombtype = 'PME-Switch',
rcoulomb = '0.8',
vdwtype = 'shift',
rvdw = '0.8',
rvdw_switch = '0.75',
DispCorr = 'Ener')
CALC_MM.generate_topology_and_g96file()
CALC_MM.generate_gromacs_run_file()
CALC_QMMM = AseQmmmManyqm(nqm_regions = 3,
qm_calculators = [CALC_QM1, CALC_QM2, CALC_QM3],
mm_calculator = CALC_MM,
link_info = 'byQM')
# link_info = 'byFILE')
SYSTEM = read_gromos('gromacs_qm.g96')
SYSTEM.set_calculator(CALC_QMMM)
DYN = BFGS(SYSTEM)
DYN.run(fmax = 0.05)
print('exiting fine')
LOG_FILE.close()
nsteps = '0',
nstfout = '1',
nstlog = '1',
nstenergy = '1',
nstlist = '1',
ns_type = 'grid',
pbc = 'xyz',
rlist = '1.15',
coulombtype = 'PME-Switch',
rcoulomb = '0.8',
vdwtype = 'shift',
rvdw = '0.8',
rvdw_switch = '0.75',
DispCorr = 'Ener')
CALC_MM.generate_topology_and_g96file()
CALC_MM.generate_gromacs_run_file()
CALC_QMMM = AseQmmmManyqm(nqm_regions=3,
qm_calculators=[CALC_QM1, CALC_QM2, CALC_QM3],
mm_calculator=CALC_MM,
link_info='byQM')
# link_info = 'byFILE')
SYSTEM = read_gromos('gromacs_qm.g96')
SYSTEM.set_calculator(CALC_QMMM)
DYN = BFGS(SYSTEM)
DYN.run(fmax=0.05)
print('exiting fine')
LOG_FILE.close()