def simulate_system(self,
equilibrate=100,
production=100,
dcd_frequency=10):
context, integrator = self.get_context()
# integrator.step(num_steps)
dummy_integrator = mm.VerletIntegrator(1 * u.femtosecond)
simulation = app.Simulation(self.topology, context.getSystem(),
dummy_integrator)
simulation.context = context
simulation.integrator = integrator
simulation.reporters.append(
app.DCDReporter('equilibration.dcd', dcd_frequency))
simulation.step(equilibrate)
simulation.reporters.clear()
simulation.reporters.append(
app.DCDReporter('production.dcd', dcd_frequency))
simulation.step(production)
self.sampler_state.update_from_context(context)
del context
def add_reporters(simulation, trajectory_file, log_every, save_every,
total_steps, continuing, checkpoint_file):
print(
f"Reporting every {log_every} steps and checkpointing on {checkpoint_file} every {save_every} steps."
)
op = "append" if continuing else "write"
print(f"Will {op} to trajectory file {trajectory_file}.\n")
basename = "output"
fp = open(f"{basename}.log", "a" if continuing else "w")
simulation.reporters.append(
app.DCDReporter(trajectory_file,
save_every,
append=continuing,
enforcePeriodicBox=False))
simulation.reporters.append(
app.CheckpointReporter(checkpoint_file, save_every))
simulation.reporters.append(StdoutLogReporter(log_every, total_steps))
simulation.reporters.append(
app.StateDataReporter(fp,
log_every,
step=True,
time=True,
potentialEnergy=True,
kineticEnergy=True,
totalEnergy=True,
temperature=True,
volume=True,
progress=True,
remainingTime=True,
speed=True,
totalSteps=total_steps,
separator='\t'))
def configure_reporters(sim, ctx, report_interval_ps, dt_ps, frames_per_h5,
wrap):
report_freq = int(report_interval_ps / dt_ps)
# Configure DCD file reporter
sim.reporters.append(app.DCDReporter(ctx.traj_file, report_freq))
# Configure contact map reporter
sim.reporters.append(
OfflineReporter(
ctx.h5_prefix,
report_freq,
wrap_pdb_file=ctx.pdb_file if wrap else None,
reference_pdb_file=ctx.reference_pdb_file,
frames_per_h5=frames_per_h5,
))
# Configure simulation output log
sim.reporters.append(
app.StateDataReporter(
ctx.log_file,
report_freq,
step=True,
time=True,
speed=True,
potentialEnergy=True,
temperature=True,
totalEnergy=True,
))
def production(self):
if os.path.exists(self.production_dcd_filename) and os.path.exists(self.production_data_filename):
return
prmtop = app.AmberPrmtopFile(self.prmtop_filename)
pdb = app.PDBFile(self.equil_pdb_filename)
system = prmtop.createSystem(nonbondedMethod=app.PME, nonbondedCutoff=CUTOFF, constraints=app.HBonds)
integrator = mm.LangevinIntegrator(self.temperature, FRICTION, TIMESTEP)
system.addForce(mm.MonteCarloBarostat(PRESSURE, self.temperature, BAROSTAT_FREQUENCY))
simulation = app.Simulation(prmtop.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.context.setPeriodicBoxVectors(*pdb.topology.getPeriodicBoxVectors())
simulation.context.setVelocitiesToTemperature(self.temperature)
print('Production.')
simulation.reporters.append(app.DCDReporter(self.production_dcd_filename, OUTPUT_FREQUENCY))
simulation.reporters.append(app.StateDataReporter(self.production_data_filename, OUTPUT_DATA_FREQUENCY, step=True, potentialEnergy=True, temperature=True, density=True))
converged = False
while not converged:
simulation.step(N_STEPS)
d = pd.read_csv(self.production_data_filename, names=["step", "U", "Temperature", "Density"], skiprows=1)
density_ts = np.array(d.Density)
[t0, g, Neff] = ts.detectEquilibration(density_ts, nskip=1000)
density_ts = density_ts[t0:]
density_mean_stderr = density_ts.std() / np.sqrt(Neff)
if density_mean_stderr < STD_ERROR_TOLERANCE:
converged = True
def equilibrate(self):
if os.path.exists(self.equil_pdb_filename):
return
prmtop = app.AmberPrmtopFile(self.prmtop_filename)
inpcrd = app.AmberInpcrdFile(self.inpcrd_filename)
system = prmtop.createSystem(nonbondedMethod=app.PME, nonbondedCutoff=CUTOFF, constraints=app.HBonds)
integrator = mm.LangevinIntegrator(self.temperature, EQUIL_FRICTION, EQUIL_TIMESTEP)
system.addForce(mm.MonteCarloBarostat(PRESSURE, self.temperature, BAROSTAT_FREQUENCY))
simulation = app.Simulation(prmtop.topology, system, integrator)
simulation.context.setPositions(inpcrd.positions)
state = simulation.context.getState(getEnergy=True)
print(state.getPotentialEnergy())
print('Minimizing.')
simulation.minimizeEnergy()
state = simulation.context.getState(getEnergy=True)
print(state.getPotentialEnergy())
simulation.context.setVelocitiesToTemperature(self.temperature)
print('Equilibrating.')
simulation.reporters.append(app.DCDReporter(self.equil_dcd_filename, OUTPUT_FREQUENCY_EQUIL))
simulation.step(N_EQUIL_STEPS)
# Re-write a better PDB with correct box sizes.
traj = md.load(self.equil_dcd_filename, top=self.prmtop_filename)[-1]
traj.save(self.equil_pdb_filename)
def run(self,
number_of_steps=15000,
report_interval=500,
filename_output_dcd="traj.dcd",
filename_output_log="openmm_equilibration.log"):
print("Running MD...")
self.simulation.reporters.append(
app.DCDReporter(filename_output_dcd, report_interval))
self.simulation.reporters.append(
app.StateDataReporter(filename_output_log,
report_interval,
step=True,
time=True,
potentialEnergy=True,
kineticEnergy=True,
totalEnergy=True,
temperature=True,
volume=True,
density=True,
progress=True,
remainingTime=True,
speed=True,
totalSteps=number_of_steps,
separator='\t'))
self.simulation.step(number_of_steps)
print("done")
def main():
print("Reading the PSF file");
# Read the PSF file
psf = app.CharmmPsfFile('g1_25mm.psf');
boxsize = 5 # Boxsize in nm
psf.setBox(boxsize*nanometer, boxsize*nanometer, boxsize*nanometer);
print("Reading the pdb file")
pdb = app.PDBFile('g1_25mm.pdb');
# Load the parameter set
lib = 'toppar/'
#params = app.CharmmParameterSet('toppar/top_all36_cgenff.rtf','toppar/par_all36_cgenff.prm','toppar/cgenff3.0.1/top_all36_cgenff.rtf','toppar/cgenff3.0.1/par_all36_cgenff.prm','g1_new.str','toppar_water_ions.str')
params = app.CharmmParameterSet('toppar/cgenff3.0.1/top_all36_cgenff.rtf','toppar/cgenff3.0.1/par_all36_cgenff.prm','g1_new.str','toppar_water_ions.str')
#platform = openmm.Platform.getPlatformByName('CUDA');
platform = openmm.Platform.getPlatformByName('Reference');
# Creating the system
system = psf.createSystem(params,
nonbondedMethod=app.PME,
nonbondedCutoff=1.2*nanometer,
switchDistance=1.0*nanometer,
ewaldErrorTolerance= 0.0001,
constraints=app.HBonds);
# Thermostat @ 298 K
system.addForce(openmm.AndersenThermostat(298*kelvin, 1/picosecond))
# adding the barostat for now
system.addForce(openmm.MonteCarloBarostat(1*bar, 298*kelvin));
integrator = openmm.VerletIntegrator(0.001*picoseconds)
simulation = app.Simulation(psf.topology, system, integrator, platform)
simulation.context.setPositions(pdb.getPositions())
simulation.minimizeEnergy(maxIterations = 500)
#nsavcrd = 10000 # save coordinates every 10 ps
#nstep = 2000000 # write dcd files every 2 ps
#nprint = 2000 # report every 2 ps
nsavcrd = 10 # save coordinates every 10 ps
nstep = 200 # write dcd files every 2 ps
nprint = 20 # report every 2 ps
firstDcdStep = nsavcrd ;
# Reporters
dcd = app.DCDReporter('g1_new.dcd', nsavcrd)
dcd._dcd = app.DCDFile(dcd._out, simulation.topology, simulation.integrator.getStepSize(), firstDcdStep, nsavcrd)
simulation.reporters.append(dcd)
simulation.reporters.append(app.StateDataReporter('g1_new.out', nprint, step=True, kineticEnergy=True, potentialEnergy=True, totalEnergy=True, temperature=True, volume=True, speed=True))
simulation.step(nstep)
simulation.reporters.pop()
simulation.reporters.pop()
dcd._out.close()
def run_dynamics(dcd_name, system, sim, equi, n_steps):
"""
Given an OpenMM Context object and options, perform molecular dynamics
calculations.
Parameters
----------
context : an OpenMM context instance
n_steps : the number of iterations for the sim
Returns
-------
"""
pdb = sim.extended_pdb
temperature = sim.temperature
friction = sim.friction
timestep = sim.timestep
integrator = mm.LangevinIntegrator(temperature, friction, timestep)
integrator.setConstraintTolerance(0.00001)
platform = mm.Platform.getPlatformByName('CUDA')
device = dcd_name[1]
dcd_name = dcd_name[0][0]
properties = {'CudaPrecision': 'mixed', 'CudaDeviceIndex': device}
simulation = app.Simulation(pdb.topology, system, integrator, platform,
properties)
simulation.context.setPositions(pdb.positions)
#zero ghost exceptions
if not sim.opt:
nonbonded_force = FSim.zero_ghost_exceptions(sim, system)
nonbonded_force.updateParametersInContext(simulation.context)
else:
nonbonded_force = system.getForce(sim.nonbonded_index)
logger.debug('Minimizing...')
simulation.minimizeEnergy()
simulation.context.setVelocitiesToTemperature(temperature)
logger.debug('Equilibrating...')
simulation.step(equi)
simulation.reporters.append(app.DCDReporter(dcd_name, 2500))
simulation.reporters.append(
app.StateDataReporter(stdout,
2500,
step=True,
potentialEnergy=True,
temperature=True,
progress=True,
remainingTime=True,
speed=True,
totalSteps=equi + n_steps,
separator='\t'))
logger.debug('Running Production...')
simulation.step(n_steps)
logger.debug('Done!')
def equilibrate(self, ff_name, water_name):
input_pdb_filename = self.get_initial_pdb_filename(ff_name, water_name)
equil_pdb_filename = self.get_equil_pdb_filename(ff_name, water_name)
equil_dcd_filename = self.get_equil_dcd_filename(ff_name, water_name)
equil_protein_pdb_filename = self.get_equil_protein_pdb_filename(
ff_name, water_name)
utils.make_path(equil_pdb_filename)
if os.path.exists(equil_pdb_filename):
return
ff = app.ForceField('%s.xml' % ff_name, '%s.xml' % water_name)
pdb = app.PDBFile(input_pdb_filename)
modeller = app.Modeller(pdb.topology, pdb.positions)
modeller.addSolvent(ff,
model=water_mapping[water_name],
padding=self.padding,
ionicStrength=self.ionic_strength)
topology = modeller.getTopology()
positions = modeller.getPositions()
system = ff.createSystem(topology,
nonbondedMethod=app.PME,
nonbondedCutoff=self.cutoff,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(self.temperature,
self.equil_friction,
self.equil_timestep)
system.addForce(
mm.MonteCarloBarostat(self.pressure, self.temperature,
self.barostat_frequency))
simulation = app.Simulation(topology, system, integrator)
simulation.context.setPositions(positions)
print('Minimizing.')
simulation.minimizeEnergy()
simulation.context.setVelocitiesToTemperature(self.temperature)
print('Equilibrating.')
simulation.reporters.append(
app.PDBReporter(equil_pdb_filename, self.n_equil_steps - 1))
simulation.reporters.append(
app.DCDReporter(equil_dcd_filename, self.equil_output_frequency))
simulation.step(self.n_equil_steps)
del simulation
del system
traj = md.load(equil_dcd_filename, top=equil_pdb_filename)[-1]
traj.save(equil_pdb_filename)
top, bonds = traj.top.to_dataframe()
atom_indices = top.index[top.chainID == 0].values
traj.restrict_atoms(atom_indices)
traj.save(equil_protein_pdb_filename)
def nvt(coords):
# Load OpenMM System
file = open(xml_filename, 'r')
serialized_system = file.read()
system = XmlSerializer.deserialize(serialized_system)
# Select Integrator
integrator = mm.LangevinIntegrator(TEMPERATURE, NVT_FRICTION,
NVT_TIME_STEP)
# Set Simulation
simulation = app.Simulation(pdb.topology, system, integrator, NVT_PLATFORM,
NVT_PROPERTIES)
#DEBUG STUFF
properties = NVT_PLATFORM.getPropertyValue(simulation.context,
'DeviceIndex')
print(properties)
print(NVT_PLATFORM.getPropertyNames())
print(NVT_PLATFORM.getSpeed())
#DEBUG STUFF
# Set Position and velocities
simulation.context.setPositions(coords)
simulation.context.setVelocitiesToTemperature(TEMPERATURE)
# Set Reporter
simulation.reporters.append(
app.DCDReporter(nvt_dcd_filename, NVT_OUTPUT_FREQ))
simulation.reporters.append(
app.StateDataReporter(nvt_data_filename,
NVT_DATA_FREQ,
step=True,
potentialEnergy=True,
temperature=True,
density=True))
state = simulation.context.getState(getEnergy=True)
if np.isnan(state.getPotentialEnergy() / kilojoule_per_mole):
raise ValueError("The Potential Energy before NVT is NaN")
print('NVT...\n')
simulation.step(NVT_STEPS)
state = simulation.context.getState(getPositions=True,
getVelocities=True,
getEnergy=True)
if np.isnan(state.getPotentialEnergy() / kilojoule_per_mole):
raise ValueError("The Potential Energy after NVT is NaN")
coords = state.getPositions()
velocities = state.getVelocities()
return coords, velocities
def build_openmm_simulation(structure,
temperature=300 * unyt.Kelvin,
pressure=1 * unyt.atm,
random_seed=42,
**kwargs):
""" Build OpenMM simulation from a parmed.Structure
Notes
-----
OpenMM does not compute a virial, which prevents us from
computing and reporting the pressure of a system.
However, the montecarlobarostat does allow for a robust method to sample
under various pressures.
"""
# First convert unyt units into something consistent for OpenMM
temperature.convert_to_units(unyt.Kelvin)
if pressure is not None:
pressure.convert_to_units(unyt.bar)
# hardcoded timestep - probably do not want to expose
timestep = 2.0 * unyt.fs
timestep.convert_to_units(unyt.ps)
integrator = openmm.LangevinIntegrator(float(temperature.value),
float((1.0 / unyt.ps).value),
float(timestep.value))
integrator.setRandomNumberSeed(random_seed)
system = structure.createSystem(nonbondedMethod=app.PME,
constraints=app.AllBonds,
nonbondedCutoff=14.0 * unit.angstroms)
if pressure is not None:
barostat = openmm.MonteCarloBarostat(float(pressure.value),
float(temperature.value), 25)
system.addForce(barostat)
sim = app.Simulation(structure.topology, system, integrator)
sim.context.setPositions(structure.positions)
sim.reporters.append(
app.StateDataReporter(open('thermo.log', 'w'),
5000,
step=True,
time=True,
potentialEnergy=True,
temperature=True,
volume=True,
speed=True))
sim.reporters.append(app.DCDReporter('trajectory.dcd', 5000))
sim.reporters.append(app.CheckpointReporter('trajectory.chk', 5000))
return sim
def npt(coords, velocities):
# Create OpenMM System
file = open(xml_filename, 'r')
serialized_system = file.read()
system = XmlSerializer.deserialize(serialized_system)
# Select Integrator
integrator = mm.LangevinIntegrator(TEMPERATURE, NPT_FRICTION,
NPT_TIME_STEP)
# Set Barostat
system.addForce(
mm.MonteCarloBarostat(PRESSURE, TEMPERATURE, BAROSTAT_FREQUENCY))
# Set Simulation
simulation = app.Simulation(prmtop.topology, system, integrator,
NPT_PLATFORM, NPT_PROPERTIES)
# Set Position and velocities
simulation.context.setPositions(coords)
simulation.context.setVelocities(velocities)
# Set Reporter
simulation.reporters.append(
app.DCDReporter(npt_dcd_filename, NPT_OUTPUT_FREQ))
simulation.reporters.append(
app.StateDataReporter(npt_data_filename,
NPT_DATA_FREQ,
step=True,
potentialEnergy=True,
temperature=True,
density=True))
state = simulation.context.getState(getEnergy=True)
if np.isnan(state.getPotentialEnergy() / kilojoule_per_mole):
raise ValueError("The Potential Energy before NPT is NaN")
print('NPT...\n')
simulation.step(NPT_STEPS)
state = simulation.context.getState(getPositions=True,
getVelocities=True,
getEnergy=True)
if np.isnan(state.getPotentialEnergy() / kilojoule_per_mole):
raise ValueError("The Potential Energy after NPT is NaN")
coords = state.getPositions()
velocities = state.getVelocities()
box = state.getPeriodicBoxVectors()
return coords, velocities, box
def testAppend(self):
"""Test appending to an existing trajectory."""
fname = tempfile.mktemp(suffix='.dcd')
pdb = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
system = ff.createSystem(pdb.topology)
# Create a simulation and write some frames to a DCD file.
integrator = mm.VerletIntegrator(0.001 * unit.picoseconds)
simulation = app.Simulation(pdb.topology, system, integrator,
mm.Platform.getPlatformByName('Reference'))
dcd = app.DCDReporter(fname, 2)
simulation.reporters.append(dcd)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)
simulation.step(10)
self.assertEqual(5, dcd._dcd._modelCount)
del simulation
del dcd
len1 = os.stat(fname).st_size
# Create a new simulation and have it append some more frames.
integrator = mm.VerletIntegrator(0.001 * unit.picoseconds)
simulation = app.Simulation(pdb.topology, system, integrator,
mm.Platform.getPlatformByName('Reference'))
dcd = app.DCDReporter(fname, 2, append=True)
simulation.reporters.append(dcd)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)
simulation.step(10)
self.assertEqual(10, dcd._dcd._modelCount)
len2 = os.stat(fname).st_size
self.assertTrue(len2 - len1 > 3 * 4 * 5 * system.getNumParticles())
del simulation
del dcd
os.remove(fname)
def production(self, ff_name, water_name):
equil_pdb_filename = self.get_equil_pdb_filename(ff_name, water_name)
production_dcd_filename = self.get_production_dcd_filename(
ff_name, water_name)
production_protein_dcd_filename = self.get_production_protein_dcd_filename(
ff_name, water_name)
utils.make_path(production_dcd_filename)
if os.path.exists(production_protein_dcd_filename):
return
ff = app.ForceField('%s.xml' % ff_name, '%s.xml' % water_name)
traj = md.load(equil_pdb_filename)
top, bonds = traj.top.to_dataframe()
atom_indices = top.index[top.chainID == 0].values
pdb = app.PDBFile(equil_pdb_filename)
system = ff.createSystem(pdb.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=self.cutoff,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(self.temperature, self.friction,
self.timestep)
system.addForce(
mm.MonteCarloBarostat(self.pressure, self.temperature,
self.barostat_frequency))
platform = mm.Platform.getPlatformByName("CUDA")
platform.setPropertyDefaultValue("CudaDeviceIndex",
os.environ["CUDA_VISIBLE_DEVICES"])
simulation = app.Simulation(pdb.topology,
system,
integrator,
platform=platform)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(self.temperature)
print('Production.')
simulation.reporters.append(
md.reporters.DCDReporter(production_protein_dcd_filename,
self.protein_output_frequency,
atomSubset=atom_indices))
simulation.reporters.append(
app.DCDReporter(production_dcd_filename, self.output_frequency))
simulation.step(self.n_steps)
def scr(input_coor_name, temperature, time_step_number, user_rand):
dir_path = 'media/files/' + user_rand + '/'
simulation_status_path = dir_path + 'simulation_status.txt'
simulation_status_during_run_path = dir_path + 'simulation_status_during_run.txt'
trajectory_path = dir_path
traj_dcd = 'trajectory.dcd'
pdb = app.PDBFile(input_coor_name)
forcefield = app.ForceField('amber99sbildn.xml', 'tip3p.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=app.NoCutoff,
constraints=app.HBonds,
rigidWater=True)
integrator = mm.LangevinIntegrator(temperature * unit.kelvin,
1.0 / unit.picoseconds,
2.0 * unit.femtoseconds)
integrator.setConstraintTolerance(0.00001)
# platform = mm.Platform.getPlatformByName('CPU')
# simulation = app.Simulation(pdb.topology, system, integrator, platform)
platform = mm.Platform.getPlatformByName('OpenCL')
properties = {'OpenCLPrecision': 'mixed'}
simulation = app.Simulation(pdb.topology, system, integrator, platform,
properties)
simulation.context.setPositions(pdb.positions)
update_simulation_status('Minimizing energy...', user_rand)
simulation.minimizeEnergy()
simulation.context.setVelocitiesToTemperature(temperature * unit.kelvin)
update_simulation_status('Equilibrating...', user_rand)
simulation.step(100)
simulation.reporters.append(
app.DCDReporter(trajectory_path + traj_dcd, 1000))
simulation.reporters.append(
app.StateDataReporter(simulation_status_during_run_path,
1000,
progress=True,
remainingTime=True,
totalSteps=time_step_number,
separator=','))
update_simulation_status('Running simulation...', user_rand)
simulation.step(time_step_number)
def liquid_analysis(mol_name, switch_dist=1.25, temp=298.15):
pdb = app.PDBFile('new.pdb')
modeller = app.Modeller(pdb.topology, pdb.positions)
forcefield = app.ForceField(f'{mol_name}.xml')
try:
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=app.PME,
ewaldErrorTolerance=0.0005,
nonbondedCutoff=(switch_dist + 0.05) *
unit.nanometer)
except ValueError:
modeller.addExtraParticles(forcefield)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=app.PME,
ewaldErrorTolerance=0.0005,
nonbondedCutoff=(switch_dist + 0.05) *
unit.nanometer)
system = opls_lj(system, switch_dist)
# FOR NPT
temp *= unit.kelvin
system.addForce(mm.MonteCarloBarostat(1 * unit.bar, temp))
integrator = mm.LangevinIntegrator(temp, 5 / unit.picosecond,
0.001 * unit.picosecond)
platform = mm.Platform.getPlatformByName('CUDA')
properties = {'CudaPrecision': 'mixed', 'CudaDeviceIndex': '0'}
simulation = app.Simulation(modeller.topology, system, integrator,
platform, properties)
simulation.context.setPositions(modeller.positions)
print('MINIMISATION STARTED')
simulation.minimizeEnergy()
print('MINIMISATION DONE')
simulation.reporters.append(app.DCDReporter('output.dcd', 1000))
simulation.reporters.append(
app.StateDataReporter('liquid.txt',
1000,
step=True,
potentialEnergy=True,
temperature=True,
density=True))
simulation.step(3000000)
np_equ_pos = simulation.context.getState(getPositions=True).getPositions()
app.PDBFile.writeFile(simulation.topology, np_equ_pos,
open('NPT_EQ_FINAL.pdb', 'w'))
def production(in_top, in_pdb, out_dcd, out_csv, temperature):
temperature = temperature * u.kelvin # TODO: recycle John's simtk.unit parser
pdb = app.PDBFile(in_pdb)
top = app.GromacsTopFile(in_top)
top.topology.setPeriodicBoxVectors(pdb.topology.getPeriodicBoxVectors())
system = top.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=CUTOFF,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(temperature, FRICTION, TIMESTEP)
system.addForce(
mm.MonteCarloBarostat(PRESSURE, temperature, BAROSTAT_FREQUENCY))
simulation = app.Simulation(top.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.context.setPeriodicBoxVectors(
*pdb.topology.getPeriodicBoxVectors())
simulation.context.setVelocitiesToTemperature(temperature)
print('Production.')
simulation.reporters.append(app.DCDReporter(out_dcd, OUTPUT_FREQUENCY))
simulation.reporters.append(
app.StateDataReporter(out_csv,
OUTPUT_DATA_FREQUENCY,
step=True,
potentialEnergy=True,
temperature=True,
density=True))
converged = False
while not converged:
simulation.step(N_STEPS)
d = pd.read_csv(out_csv,
names=["step", "U", "Temperature", "Density"],
skiprows=1)
density_ts = np.array(d.Density)
[t0, g, Neff] = ts.detectEquilibration(density_ts, nskip=1000)
density_ts = density_ts[t0:]
density_mean_stderr = density_ts.std() / np.sqrt(Neff)
if density_mean_stderr < STD_ERROR_TOLERANCE:
converged = True
def equilibrate(self):
self.ran_equilibrate = True
utils.make_path('equil/')
self.equil_dcd_filename = "equil/" + self.identifier + "_equil.dcd"
self.equil_pdb_filename = "equil/" + self.identifier + "_equil.pdb"
utils.make_path(self.equil_pdb_filename)
if os.path.exists(self.equil_pdb_filename):
return
positions = self.packed_trj.openmm_positions(0)
topology = self.packed_trj.top.to_openmm()
topology.setUnitCellDimensions(
mm.Vec3(*self.packed_trj.unitcell_lengths[0]) * u.nanometer)
ff = self.ffxml
system = ff.createSystem(topology,
nonbondedMethod=app.PME,
nonbondedCutoff=self.cutoff,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(self.temperature,
self.equil_friction,
self.equil_timestep)
system.addForce(
mm.MonteCarloBarostat(self.pressure, self.temperature,
self.barostat_frequency))
simulation = app.Simulation(topology, system, integrator)
simulation.context.setPositions(positions)
print('Minimizing.')
simulation.minimizeEnergy()
simulation.context.setVelocitiesToTemperature(self.temperature)
print('Equilibrating.')
simulation.reporters.append(
app.DCDReporter(self.equil_dcd_filename,
self.equil_output_frequency))
simulation.step(self.n_equil_steps)
# Re-write a better PDB with correct box sizes.
traj = md.load(self.equil_dcd_filename, top=self.box_pdb_filename)[-1]
traj.save(self.equil_pdb_filename)
def simulation(filepath, outpath, nsteps, gpu=True):
prmtop = app.AmberPrmtopFile(f'{filepath}.prmtop')
inpcrd = app.AmberInpcrdFile(f'{filepath}.inpcrd')
forcefield = app.ForceField('amber14-all.xml', 'amber14/tip3p.xml')
modeller = app.Modeller(prmtop.topology, inpcrd.positions)
modeller.addSolvent(forcefield, padding=1.4 * unit.nanometer)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0 * unit.nanometer,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(310.15 * unit.kelvin,
1.0 / unit.picosecond,
0.002 * unit.picosecond)
if gpu:
platform = 'CUDA'
else:
platform = 'CPU'
platform = mm.Platform.getPlatformByName(platform)
properties = {'Precision': 'double'}
simulation = app.Simulation(modeller.topology, system, integrator,
platform, properties)
simulation.context.setPositions(modeller.positions)
simulation.minimizeEnergy()
if nsteps != 0:
simulation.reporters.append(
app.DCDReporter(f'{outpath}/traj.dcd', 25000))
simulation.reporters.append(
app.StateDataReporter(f'{outpath}/sim.log',
25000,
step=True,
potentialEnergy=True,
temperature=True))
simulation.reporters.append(
app.CheckpointReporter(f'{outpath}/traj.chk', 250000))
simulation.step(nsteps)
positions = simulation.context.getState(
getPositions=True).getPositions()
app.PDBFile.writeFile(simulation.topology, positions,
open(f'{outpath}/output.pdb', 'w'))
potential = simulation.context.getState(
getEnergy=True).getPotentialEnergy().value_in_unit(unit.kilojoule /
unit.mole)
return potential
def simulation_ESMACS(filepath, outpath, nsteps):
prmtop = app.AmberPrmtopFile(f'{filepath}_sol.prmtop')
inpcrd = app.AmberInpcrdFile(f'{filepath}_sol.inpcrd')
system = prmtop.createSystem(nonbondedMethod=app.PME, nonbondedCutoff=1.0*unit.nanometer,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picosecond, 0.002*unit.picosecond)
platform = mm.Platform.getPlatformByName('CUDA')
properties = {'Precision': 'double'}
simulation = app.Simulation(prmtop.topology, system, integrator, platform, properties)
simulation.context.setPositions(inpcrd.positions)
if inpcrd.boxVectors is not None:
simulation.context.setPeriodicBoxVectors(*inpcrd.boxVectors)
simulation.minimizeEnergy()
simulation.reporters.append(app.DCDReporter(f'{outpath}/traj.dcd', 50000)) # snapshot at every 100 ps
simulation.reporters.append(app.StateDataReporter(f'{outpath}/sim.log', 5000, step=True,
potentialEnergy=True, temperature=True)) # reporting at every 10 ps
simulation.reporters.append(app.CheckpointReporter(f'{outpath}/traj.chk', 250000)) # checkpoint at every 0.5 ns
simulation.step(nsteps)
positions = simulation.context.getState(getPositions=True).getPositions()
app.PDBFile.writeFile(simulation.topology, positions, open(f'{outpath}/output.pdb', 'w'))
def scr_for_checks(input_coor_name, user_rand, full_check=False):
pdb = app.PDBFile(input_coor_name)
forcefield = app.ForceField('amber99sbildn.xml', 'tip3p.xml')
# The following line causes an error (when we do not perform "fix pdb")
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=app.NoCutoff,
constraints=app.HBonds,
rigidWater=True)
if full_check:
integrator = mm.LangevinIntegrator(300 * unit.kelvin,
1.0 / unit.picoseconds,
2.0 * unit.femtoseconds)
integrator.setConstraintTolerance(0.00001)
# platform = mm.Platform.getPlatformByName('CPU')
# simulation = app.Simulation(pdb.topology, system, integrator, platform)
platform = mm.Platform.getPlatformByName('OpenCL')
properties = {'OpenCLPrecision': 'mixed'}
simulation = app.Simulation(pdb.topology, system, integrator, platform,
properties)
simulation.context.setPositions(pdb.positions)
# Minimizing
simulation.minimizeEnergy()
simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)
# Equilibrating
simulation.step(100)
simulation.reporters.append(
app.DCDReporter(
'media/files/' + user_rand + '/' + 'scr_for_checks.dcd', 1000))
# Running Production
simulation.step(1000)
def configure_reporters(
sim: omm.app.Simulation,
ctx: SimulationContext,
cfg: OpenMMConfig,
report_steps: int,
frames_per_h5: int,
):
# Configure DCD file reporter
sim.reporters.append(app.DCDReporter(ctx.traj_file, report_steps))
# Configure contact map reporter
sim.reporters.append(
OfflineReporter(
ctx.h5_prefix,
report_steps,
frames_per_h5=frames_per_h5,
wrap_pdb_file=ctx.pdb_file if cfg.wrap else None,
reference_pdb_file=ctx.reference_pdb_file,
openmm_selection=cfg.openmm_selection,
mda_selection=cfg.mda_selection,
threshold=cfg.threshold,
contact_map=cfg.contact_map,
point_cloud=cfg.point_cloud,
fraction_of_contacts=cfg.fraction_of_contacts,
))
# Configure simulation output log
sim.reporters.append(
app.StateDataReporter(
ctx.log_file,
report_steps,
step=True,
time=True,
speed=True,
potentialEnergy=True,
temperature=True,
totalEnergy=True,
))
def simulation(filepath, outpath, nsteps):
prmtop = app.AmberPrmtopFile(f'{filepath}.prmtop')
inpcrd = app.AmberInpcrdFile(f'{filepath}.inpcrd')
forcefield = app.ForceField('amber14-all.xml', 'amber14/tip3p.xml') # gaff/gaff2/other ligand ff also required here or it may complain for 'com' or 'lig'
modeller = app.Modeller(prmtop.topology, inpcrd.positions)
modeller.addSolvent(forcefield, padding=1.4*unit.nanometer)
system = forcefield.createSystem(modeller.topology, nonbondedMethod=app.PME, nonbondedCutoff=1.0*unit.nanometer,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picosecond, 0.002*unit.picosecond)
platform = mm.Platform.getPlatformByName('CUDA')
properties = {'Precision': 'double'}
simulation = app.Simulation(modeller.topology, system, integrator, platform, properties)
simulation.context.setPositions(modeller.positions)
simulation.minimizeEnergy()
if nsteps != 0:
simulation.reporters.append(app.DCDReporter(f'{outpath}_traj.dcd', 25000)) # snapshot at every 50 ps
simulation.reporters.append(nosol.NewPDBReporter(f'{outpath}_system_nosol.pdb', 25000)) # snapshot at every 50 ps
simulation.reporters.append(app.StateDataReporter(f'{outpath}_sim.log', 25000, step=True,
potentialEnergy=True, temperature=True)) # reporting at every 50 ps
simulation.reporters.append(app.CheckpointReporter(f'{outpath}_traj.chk', 250000)) # checkpoint at every 0.5 ns
simulation.step(nsteps)
positions = simulation.context.getState(getPositions=True).getPositions()
app.PDBFile.writeFile(simulation.topology, positions, open(f'{outpath}_output.pdb', 'w'))
# Return potential energy at the end of the simulation
# potential = simulation.context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(unit.kilojoule/unit.mole)
# return potential
# Return mean potential energy during the simulation
with open(f'{outpath}_sim.log','r') as log_file:
lines = log_file.readlines()
mean = 0
for i in range(1,len(lines)):
potential = float(lines[i].split(',')[1])
mean = mean + potential
potential = mean/(len(lines)-1)
return potential
def equilibrate(in_top, in_gro, out_dcd, out_pdb, temperature):
temperature = temperature * u.kelvin # TODO: recycle John's simtk.unit parser
gro = app.GromacsGroFile(in_gro)
top = app.GromacsTopFile(in_top,
unitCellDimensions=gro.getUnitCellDimensions())
system = top.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=CUTOFF,
constraints=app.HBonds)
integrator = mm.LangevinIntegrator(temperature, EQUIL_FRICTION,
EQUIL_TIMESTEP)
system.addForce(
mm.MonteCarloBarostat(PRESSURE, temperature, BAROSTAT_FREQUENCY))
simulation = app.Simulation(top.topology, system, integrator)
simulation.context.setPositions(gro.positions)
state = simulation.context.getState(getEnergy=True)
print(state.getPotentialEnergy())
print('Minimizing.')
simulation.minimizeEnergy()
state = simulation.context.getState(getEnergy=True)
print(state.getPotentialEnergy())
simulation.context.setVelocitiesToTemperature(temperature)
print('Equilibrating.')
simulation.reporters.append(
app.DCDReporter(out_dcd, OUTPUT_FREQUENCY_EQUIL))
simulation.step(N_EQUIL_STEPS)
# Re-write a better PDB with correct box sizes.
traj = md.load(out_dcd, top=in_gro)[-1]
traj.save(out_pdb)
def gas_analysis(mol_name, temp=298.15):
temp *= unit.kelvin
pdb = app.PDBFile(mol_name + '.pdb')
modeller = app.Modeller(pdb.topology, pdb.positions)
forcefield = app.ForceField(mol_name + '.xml')
try:
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=app.NoCutoff,
constraints=None)
except ValueError:
modeller.addExtraParticles(forcefield)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=app.NoCutoff,
constraints=None)
system = opls_lj(system)
integrator = mm.LangevinIntegrator(temp, 5 / unit.picosecond,
0.0005 * unit.picosecond)
simulation = app.Simulation(modeller.topology, system, integrator)
simulation.context.setPositions(modeller.positions)
print(f'Results for: {mol_name}.')
simulation = minimise(simulation, 100)
simulation.reporters.append(app.DCDReporter('gas_output.dcd', 1000))
simulation.reporters.append(
app.StateDataReporter('gas.txt',
1000,
step=True,
temperature=True,
potentialEnergy=True,
density=True,
totalSteps=10000,
totalEnergy=True))
simulation.step(6000000)
def configure_reporters(sim, ctx, report_interval_ps, dt_ps, frames_per_h5,
wrap):
# Configure reporters
report_freq = int(report_interval_ps / dt_ps)
# Overwriting sim.reporters: we're writing new report files but with same
# simulation state
sim.reporters = []
# Configure DCD file reporter
sim.reporters.append(app.DCDReporter(ctx.traj_file, report_freq))
# Configure contact map reporter
senders = [ctx.scp_sender] if ctx.scp_sender is not None else []
sim.reporters.append(
SparseContactMapReporter(
ctx.h5_prefix,
report_freq,
wrap_pdb_file=ctx.pdb_file if wrap else None,
reference_pdb_file=ctx.reference_pdb_file,
senders=senders,
batch_size=frames_per_h5,
))
# Configure simulation output log
sim.reporters.append(
app.StateDataReporter(
ctx.log_file,
report_freq,
step=True,
time=True,
speed=True,
potentialEnergy=True,
temperature=True,
totalEnergy=True,
))
def run_steered_md(
temperature,
checkpoint_in_file,
csv_out_file,
dat_out_file,
pdb_out_file,
traj_out_file,
startdist,
spring_constant=50,
force_constant_chunk=0.1,
init_velocity=0.00001,
gpu_id=0,
):
if os.path.isfile(pdb_out_file):
return
spring_k = spring_constant * u.kilocalorie / (u.mole * u.angstrom *
u.angstrom)
dist_in = startdist * u.angstrom # in angstrom
dist_fin = (startdist + 2.5) * u.angstrom # in angstrom
steps_per_move = 200
velocity = init_velocity * u.angstrom
# Platform definition
platform = mm.Platform_getPlatformByName("OpenCL")
platformProperties = {}
platformProperties["OpenCLPrecision"] = "mixed"
platformProperties["OpenCLDeviceIndex"] = gpu_id
print("loading pickle")
pickle_in = open("complex_system.pickle", "rb")
combined_pmd = pickle.load(pickle_in)[0]
print(combined_pmd)
pickle_in.close()
keyInteraction = cal_ints.find_interaction()
print(keyInteraction)
# Get indexes of heavy atoms in chunk
Chunk_Heavy_Atoms = duck_stuff.getHeavyAtomsInSystem(combined_pmd)
# Setting System
system = combined_pmd.createSystem(
nonbondedMethod=app.PME,
nonbondedCutoff=9 * u.angstrom,
constraints=app.HBonds,
hydrogenMass=None,
)
# Apply force on all havy atoms of chunk
duck_stuff.applyHarmonicPositionalRestraints(system, force_constant_chunk,
combined_pmd.positions,
Chunk_Heavy_Atoms)
# Integrator
integrator = mm.LangevinIntegrator(temperature, 4 / u.picosecond,
0.002 * u.picosecond)
# Setting Simulation object and loading the checkpoint
simulation = app.Simulation(combined_pmd.topology, system, integrator,
platform, platformProperties)
simulation.loadCheckpoint(checkpoint_in_file)
# SMD force definition
pullforce = mm.CustomExternalForce("k_sp*0.5*(R-R0)^2; \
R = periodicdistance(x, y, z, x0, y0, z0);"
)
pullforce.addPerParticleParameter("k_sp")
pullforce.addGlobalParameter("x0", 0.0 * u.nanometer)
pullforce.addGlobalParameter("y0", 0.0 * u.nanometer)
pullforce.addGlobalParameter("z0", 0.0 * u.nanometer)
pullforce.addGlobalParameter("R0", 0.0 * u.nanometer)
pullforce.addParticle(keyInteraction[1], [spring_k])
system.addForce(pullforce)
# Redefine integrator and simulation, and load checkpoint with new-updated system
integrator = mm.LangevinIntegrator(temperature, 4 / u.picosecond,
0.002 * u.picosecond)
simulation = app.Simulation(combined_pmd.topology, system, integrator,
platform, platformProperties)
simulation.loadCheckpoint(checkpoint_in_file)
# Initializing energy
work_val_old = u.Quantity(value=0, unit=u.kilocalorie / u.mole)
# Number of big steps and pull distance
steps = int(round((dist_fin - dist_in) / velocity) / steps_per_move)
pull_distance = velocity * steps_per_move
# Reporters and duck.dat file
simulation.reporters.append(
app.StateDataReporter(
csv_out_file,
steps_per_move,
step=True,
time=True,
totalEnergy=True,
kineticEnergy=True,
potentialEnergy=True,
temperature=True,
density=True,
progress=True,
totalSteps=steps_per_move * steps,
speed=True,
))
simulation.reporters.append(app.DCDReporter(traj_out_file, 100000))
f = open(dat_out_file, "w")
# Production in N steps with the update every 200 steps (2 pm)
for i in range(steps):
# Get current state tu update the system
state = simulation.context.getState(getPositions=True)
pos_keyInt = state.getPositions()
keyInteraction_pos = [
pos_keyInt[keyInteraction[0]],
pos_keyInt[keyInteraction[1]],
]
# Get radius of starting point and end point
R_val = dist_in + float(i + 1) * pull_distance
R_val_start = dist_in + float(i) * pull_distance
# Get distance of main interaction
keyInteraction_dist = np.linalg.norm(keyInteraction_pos[0] -
keyInteraction_pos[1])
print(keyInteraction_dist)
# Updated system
simulation.context.setParameter("x0", keyInteraction_pos[0][0])
simulation.context.setParameter("y0", keyInteraction_pos[0][1])
simulation.context.setParameter("z0", keyInteraction_pos[0][2])
simulation.context.setParameter("R0", R_val)
# Calculate force F = -k * x
force_val = -spring_k * (keyInteraction_dist - R_val)
# Make step
simulation.step(steps_per_move)
# Calculate work for difference in potential energy in tranzition
# W = EK_end - EK_start
# EK = 0.5 * k * x^2
spr_energy_end = 0.5 * spring_k * (keyInteraction_dist - R_val)**2
spr_energy_start = 0.5 * spring_k * (keyInteraction_dist -
R_val_start)**2
work_val = work_val_old + spr_energy_end - spr_energy_start
work_val_old = work_val
# Write duck.dat file
f.write(
str(i) + " " + str(R_val) + " " + str(keyInteraction_dist) + " " +
str(force_val) + " " + str(work_val) + "\n")
f.close()
# Save state in PDB file
positions = simulation.context.getState(getPositions=True).getPositions()
app.PDBFile.writeFile(simulation.topology, positions,
open(pdb_out_file, "w"))
# Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not specify
# the platform to use the default (fastest) platform
platform = mm.Platform.getPlatformByName('CUDA')
prop = dict(CudaPrecision='mixed') # Use mixed single/double precision
# Create the Simulation object
sim = app.Simulation(ala5_gas.topology, system, integrator, platform, prop)
# Set the particle positions
sim.context.setPositions(ala5_crds.positions)
# Minimize the energy
print('Minimizing energy')
sim.minimizeEnergy(maxIterations=500)
# Set up the reporters to report energies and coordinates every 100 steps
sim.reporters.append(
StateDataReporter(sys.stdout,
100,
step=True,
potentialEnergy=True,
kineticEnergy=True,
temperature=True,
volume=True,
density=True))
sim.reporters.append(app.DCDReporter('ala5_gb.dcd', 100))
# Run dynamics
print('Running dynamics')
sim.step(10000)
forcefield = app.ForceField(ff_filename)
system = forcefield.createSystem(topology,
nonbondedMethod=app.CutoffPeriodic, nonbondedCutoff=cutoff,
switchDistance=r_switch, ignoreExternalBonds=True, residueTemplates=templates)
#for i in range(system.getNumForces()):
# force = system.getForce(i)
# force.setForceGroup(i)
integrator = omm.LangevinIntegrator(temperature, collision_rate, timestep)
simulation = app.Simulation(topology, system, integrator)
simulation.context.setPositions(positions)
simulation.reporters.append(app.DCDReporter(traj_name, nsteps_out))
simulation.reporters.append(app.StateDataReporter(log_name, nsteps_out,
step=True, potentialEnergy=True))
simulation.reporters.append(sop.additional_reporters.ForceReporter(name + "_forces_{}.dat".format(traj_idx), nsteps_out))
simulation.step(100*nsteps_out + 5)
sigma_ply, eps_ply, mass_ply, bonded_params = sop.build_ff.toy_polymer_params()
r0, kb, theta0, ka = bonded_params
sigma_ply_nm = sigma_ply/unit.nanometer
r0_wca_nm = sigma_ply_nm*(2**(1./6))
eps_ply_kj = eps_ply/unit.kilojoule_per_mole
kb_kj = kb/(unit.kilojoule_per_mole/(unit.nanometer**2))
ka_kj = (ka/(unit.kilojoule_per_mole/(unit.radian**2)))
pfreq = cmd.pfreq if cmd.pfreq is not None else 2000
else:
# Time step is 2 fs
# 500.000 steps give 1 ns
wfreq = cmd.wfreq if cmd.wfreq is not None else 5000
pfreq = cmd.pfreq if cmd.pfreq is not None else 5000
eq_dcd = rootname + '.dcd'
if cmd.continuation:
eq_dcd = get_part_filename(eq_dcd)
eq_log = rootname + '.log'
if cmd.continuation:
eq_log = get_part_filename(eq_log)
dcd = app.DCDReporter(eq_dcd, wfreq)
cpt = app.CheckpointReporter(eq_cpt, wfreq)
state = app.StateDataReporter(eq_log,
pfreq,
step=True,
time=True,
progress=True,
potentialEnergy=True,
kineticEnergy=True,
temperature=True,
remainingTime=True,
speed=True,
totalSteps=n_steps,
separator='\t')