def run(in_parms):
"Runs AMBER with in_parms"
parms = copy.deepcopy(in_parms)
name = parms['output_name']
config = name + ".config"
if util.is_same_dict_in_file(in_parms, config):
print "simulation already run."
return
input_top = parms['topology']
new_top = name + '.top'
shutil.copy(input_top, new_top)
input_crd = parms['input_crds']
if input_crd.endswith('.crd'):
new_crd = name + '.in.crd'
else:
new_crd = name + '.in.rst'
shutil.copy(input_crd, new_crd)
if 'n_step_minimization' in parms:
rst = name + ".crd"
else:
rst = name + ".rst"
trj = name + ".trj"
vel = name + ".vel"
ene = name + ".ene"
inf = name + ".inf"
sander_out = name + ".sander.out"
sander_in = name + ".sander.in"
open(sander_in, "w").write(make_sander_input_file(parms))
cmd = "sander -O -i %s -o %s -p %s -c %s -r %s -x %s -v %s -e %s -inf %s" \
% (sander_in, sander_out, new_top, new_crd, rst, trj, vel, ene, inf)
if parms['constraint_pdb']:
cmd += " -ref %s" % parms['constraint_pdb'].replace('.pdb', '.crd')
sh_script = name + '.sh'
open(sh_script, "w").write(cmd)
S_IRWXU = stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR
os.chmod(sh_script, S_IRWXU)
stopwatch = util.Timer()
os.system(cmd)
stopwatch.stop()
open(name + '.time', 'w').write(stopwatch.str())
error_log = open(sander_out, "r").readlines()
is_error = False
for line in error_log:
if 'FATAL' in line:
is_error = True
break
if len(error_log) <= 1:
is_error = True
if not is_error:
util.write_dict(in_parms, config)
def pulse(in_parms, n_step_per_pulse, reset_vel_func):
config = in_parms['output_name'] + ".config"
if util.is_same_dict_in_file(in_parms, config):
print "simulation already run."
return
name = in_parms['output_name']
shutil.copy(in_parms['topology'], name + '.psf')
if in_parms['constraint_pdb']:
shutil.copy(in_parms['constraint_pdb'], name + '.constraint')
n_pulse = in_parms['n_step_dynamics'] // n_step_per_pulse
n_step_list = [n_step_per_pulse for i in range(n_pulse)]
n_excess_step = in_parms['n_step_dynamics'] % n_step_per_pulse
if n_excess_step > 0:
n_pulse += 1
n_step_list.append(n_excess_step)
pulse_in_coor = util.insert_path(in_parms['input_crds'], '..')
pulse_in_vel = util.insert_path(in_parms['input_vels'], '..')
stopwatch = util.Timer()
pulses = ["pulse%d" % i for i in range(n_pulse)]
for pulse, n_step in zip(pulses, n_step_list):
util.goto_dir(pulse)
pulse_parms = copy.deepcopy(in_parms)
pulse_parms['topology'] = util.insert_path(in_parms['topology'], '..')
pulse_parms['n_step_dynamics'] = n_step
if 'constraint_pdb' in pulse_parms and pulse_parms['constraint_pdb']:
pulse_parms['constraint_pdb'] = util.insert_path(in_parms['constraint_pdb'], '..')
pulse_parms['input_crds'] = pulse_in_coor
pulse_parms['input_vels'] = pulse_in_vel
soup = SoupFromRestartFiles(pulse_parms['topology'],
pulse_parms['input_crds'],
pulse_parms['input_vels'])
reset_vel_func(soup)
pulse_parms['input_vels'] = name + ".in.vel"
write_soup_to_vel(soup, pulse_parms['input_vels'])
run(pulse_parms)
pulse_in_coor = '../%s/%s.coor' % (pulse, name)
pulse_in_vel = '../%s/%s.vel' % (pulse, name)
os.chdir('..')
stopwatch.stop()
open(name + '.time', 'w').write(stopwatch.str())
merge_simulations(name, pulses)
for pulse in pulses: os.system('rm -rf %s' % pulse)
util.write_dict(in_parms, config)
def run_simulation_with_parameters(parms):
"""
Carries out simulations based on parms
"""
# For housekeeping, the parms dictionary is written to a
# .config file. As an Exception is thrown if simulation failed,
# the existence of an equivalent .config file is an indicator
# that the simulation has already successfully run.
config = parms['output_basename'] + ".config"
if util.is_same_dict_in_file(parms, config):
print "Skipping: simulation already run."
return
md_module = get_md_module(parms['force_field'])
md_module.run(parms)
# No exceptions were thrown - write .config file.
util.write_dict(config, parms)
def run(in_parms):
"Read parms and creates the appropriate NAMD input files for simulation"
name = in_parms['output_name']
input = name + ".in"
output = name + ".out"
config = name + ".config"
parms = copy.deepcopy(in_parms)
if util.is_same_dict_in_file(parms, config):
print "simulation already run."
return
shutil.copy(parms['topology'], name + '.psf')
if parms['constraint_pdb']:
shutil.copy(parms['constraint_pdb'], name + '.constraint')
if 'force_field' in parms:
if parms['force_field'] == "CHARMM":
parms['parameter'] = 'parms/charmm22.parameter'
parms['psf_type'] = 'paraTypeCharmm on'
elif parms['force_field'] == "OPLS":
parms['parameter'] = 'parms/opls.parameter'
parms['psf_type'] = 'paraTypeXplor on'
else:
raise "Can't identify force-field"
parms['module_dir'] = module_dir
open(input, "w").write(make_namd_input_file(parms))
stopwatch = util.Timer()
os.system("namd2 %s > %s" % (input, output))
stopwatch.stop()
open(name + '.time', 'w').write(stopwatch.str())
for line in open(output, "r"):
if 'ERROR' in line and 'Info' not in line:
raise "NAMD failure: '%s'" % line.replace("\n", "")
util.write_dict(in_parms, config)
def pulse(
force_field, in_basename, basename, n_step, pulse_fn,
n_step_per_pulse=100, restraint_pdb="", restraint_force=None):
"""
Runs a pulse simulation that uses the restart-file modification
strategy to manage a steered-molecular dynamics simulation.
The pulsed approacha pplies external forces in pulses, which is
practically carried out be running short constant-energy
simulations and directly modifying the restart velocities
between each simulation.
Pulse simulations has certain advantages: for instance, the
system can respond to the forces between pulses, and the
incredibly flexibility in applying forces. The disadvantage is
the costly setup which is hopefully, mitigated by this library.
Reference: Bosco K. Ho and David A. Agard (2010) "An improved
strategy for generating forces in steered molecular dynamics:
the mechanical unfolding of titin, e2lip3 and ubiquitin" PLoS
ONE 5(9):e13068.
"""
# Grab the simulation prameters for a constant energy
# simulation. Constant energy is preferred as we want to ensure
# energy changes come only from our velocity modification.
top, crds, vels = get_restart_files(in_basename)
# use dummy top and crds, which will be overriden
overall_config_parms = fetch_simulation_parameters(
force_field, top, crds, restraint_pdb,
'constant_energy', basename, restraint_force)
overall_config_parms.update({
'input_md_name': in_basename,
'input_vels': vels,
'n_step_dynamics': n_step,
'n_step_per_snapshot': n_step_per_pulse // 2,
'n_step_per_pulse': n_step_per_pulse
})
# Check if the simulation has already run as the config
# file is not written until the very end
config = basename + ".config"
if util.is_same_dict_in_file(overall_config_parms, config):
print "Skipping: pulsing simulation already run."
return
# The overall_config_parms will be written out at the end.
# We make a copy for internal use
pulse_parms = copy.deepcopy(overall_config_parms)
# Calculate steps for each pulse, esp for last step
n_pulse = pulse_parms['n_step_dynamics'] / n_step_per_pulse
n_step_list = [n_step_per_pulse for i in range(n_pulse)]
n_excess_step = pulse_parms['n_step_dynamics'] % n_step_per_pulse
if n_excess_step > 0:
n_pulse += 1
n_step_list.append(n_excess_step)
# Prepare restart files for first step
pulse_parms['topology'] = os.path.abspath(pulse_parms['topology'])
in_basename = pulse_parms['input_md_name']
pulse_parms['input_md_name'] = os.path.abspath(in_basename)
# Now loop through pulses
timer = util.Timer()
save_dir = os.getcwd()
pulses = ["pulse%d" % i for i in range(n_pulse)]
for pulse, n_step in zip(pulses, n_step_list):
print "Pulse: %s/%d" % (pulse, n_pulse)
os.chdir(save_dir)
util.goto_dir(pulse)
pulse_parms['n_step_dynamics'] = n_step
soup = soup_from_restart_files(pulse_parms['input_md_name'])
# Apply forces by modifying the velocities directly
pulse_fn(soup)
crds, vels = write_soup_to_crds_and_vels(
force_field, soup, basename + '.pulse.in')
pulse_parms['input_crds'] = crds
pulse_parms['input_vels'] = vels
run_simulation_with_parameters(pulse_parms)
# Setup new restart files based on just-finished pulse
pulse_parms['input_md_name'] = os.path.abspath(basename)
os.chdir(save_dir)
merge_simulations(force_field, basename, pulses)
# cleanup pulses after merging
util.clean_fname(*pulses)
# everything worked, no exceptions thrown
open(basename+'.time', 'w').write(timer.str()+'\n')
util.write_dict(config, overall_config_parms)
