freq = max(1, math.floor(cmd.ladder_num_steps / 10))
if cmd.hmr:
# Time step is 5 fs
xyz_freq = cmd.xyz_freq if cmd.xyz_freq is not None else freq
log_freq = cmd.log_freq if cmd.log_freq is not None else freq
else:
# Time step is 2 fs
xyz_freq = cmd.xyz_freq if cmd.xyz_freq is not None else freq
log_freq = cmd.log_freq if cmd.log_freq is not None else freq
# Calculate total simulation length in steps
n_stages = math.ceil(cmd.temperature / cmd.ladder_step_temperature)
n_total_steps = n_stages * cmd.ladder_num_steps
# Setup Reporters
dcd_fname = _utils.make_fname(rootname + '.dcd')
cpt_fname = _utils.make_fname(rootname + '.cpt')
log_fname = _utils.make_fname(rootname + '.log')
dcd = app.DCDReporter(dcd_fname, xyz_freq)
cpt = app.CheckpointReporter(cpt_fname, xyz_freq)
state = app.StateDataReporter(log_fname,
log_freq,
step=True,
potentialEnergy=True,
kineticEnergy=True,
temperature=True,
progress=True,
remainingTime=True,
totalSteps=n_total_steps,
speed=True,
separator='\t')
logging.info('Writing system without dummy (restraint) atoms')
system = forcefield.createSystem(model.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=md_nbct,
constraints=md_cstr,
hydrogenMass=md_hamu,
ewaldErrorTolerance=0.0005,
rigidWater=True)
integrator = mm.LangevinIntegrator(md_temp, md_fric, md_step)
simulation = app.Simulation(model.topology, system, integrator)
simulation.context.setPositions(xyz[:n_ini_atoms])
simulation.context.setVelocities(vel[:n_ini_atoms])
simulation.context.setPeriodicBoxVectors(vx, vy, vz)
xml_fname = _utils.make_fname(rootname + '_noDUM' + '.xml')
logging.info(f'Writing dummy-less state to \'{xml_fname}\'')
simulation.saveState(xml_fname)
# Write last frame as mmCIF
cif_fname = _utils.make_fname(rootname + '_noDUM' + '.cif')
logging.info(f'Writing dummy-less structure to \'{cif_fname}\'')
with open(cif_fname, 'w') as handle:
app.PDBxFile.writeFile(model.topology,
xyz[:n_ini_atoms],
handle,
keepIds=True)
logging.info('Finished')
# Minimize
simulation = app.Simulation(structure.topology, system, integrator, platform,
plat_properties)
simulation.context.setPositions(structure.positions)
state = simulation.context.getState(getEnergy=True)
energy = state.getPotentialEnergy().value_in_unit_system(units.md_unit_system)
logging.info('Initial Potential Energy: {:10.3f}'.format(energy))
logging.info('Running minimization ...')
simulation.minimizeEnergy(maxIterations=cmd.iterations)
state = simulation.context.getState(getEnergy=True, getPositions=True)
energy = state.getPotentialEnergy().value_in_unit_system(units.md_unit_system)
logging.info('Final Potential Energy: {:10.3f}'.format(energy))
# Write minimized structure
if cmd.output:
if not cmd.output.endswith('.cif'):
_fname = cmd.output + '.cif'
else:
_fname = cmd.output
else:
_fname = fname + '_EM' + '.cif'
cif_fname = _utils.make_fname(_fname)
logging.info('Writing structure to \'{}\''.format(cif_fname))
with open(cif_fname, 'w') as handle:
minimized_positions = state.getPositions()
app.PDBxFile.writeFile(structure.topology, minimized_positions, handle)