def openmm_simulate_charmm_nvt(top_file,
pdb_file,
check_point=None,
GPU_index=0,
output_traj="output.dcd",
output_log="output.log",
output_cm=None,
report_time=10 * u.picoseconds,
sim_time=10 * u.nanoseconds):
"""
Start and run an OpenMM NVT simulation with Langevin integrator at 2 fs
time step and 300 K. The cutoff distance for nonbonded interactions were
set at 1.2 nm and LJ switch distance at 1.0 nm, which commonly used with
Charmm force field. Long-range nonbonded interactions were handled with PME.
Parameters
----------
top_file : topology file (.top, .prmtop, ...)
This is the topology file discribe all the interactions within the MD
system.
pdb_file : coordinates file (.gro, .pdb, ...)
This is the molecule configuration file contains all the atom position
and PBC (periodic boundary condition) box in the system.
check_point : None or check point file to load
GPU_index : Int or Str
The device # of GPU to use for running the simulation. Use Strings, '0,1'
for example, to use more than 1 GPU
output_traj : the trajectory file (.dcd)
This is the file stores all the coordinates information of the MD
simulation results.
output_log : the log file (.log)
This file stores the MD simulation status, such as steps, time, potential
energy, temperature, speed, etc.
output_cm : the h5 file contains contact map information
report_time : 10 ps
The program writes its information to the output every 10 ps by default
sim_time : 10 ns
The timespan of the simulation trajectory
"""
top = pmd.load_file(top_file, xyz=pdb_file)
system = top.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=1.2 * u.nanometer,
switchDistance=1.0 * u.nanometer,
constraints=app.HBonds)
dt = 0.002 * u.picoseconds
integrator = omm.LangevinIntegrator(300 * u.kelvin, 1 / u.picosecond, dt)
try:
platform = omm.Platform_getPlatformByName("CUDA")
properties = {'DeviceIndex': str(GPU_index), 'CudaPrecision': 'mixed'}
except Exception:
platform = omm.Platform_getPlatformByName("OpenCL")
properties = {'DeviceIndex': str(GPU_index)}
simulation = app.Simulation(top.topology, system, integrator, platform,
properties)
simulation.context.setPositions(top.positions)
simulation.minimizeEnergy()
report_freq = int(report_time / dt)
simulation.context.setVelocitiesToTemperature(10 * u.kelvin,
random.randint(1, 10000))
simulation.reporters.append(app.DCDReporter(output_traj, report_freq))
if output_cm:
simulation.reporters.append(ContactMapReporter(output_cm, report_freq))
simulation.reporters.append(
app.StateDataReporter(output_log,
report_freq,
step=True,
time=True,
speed=True,
potentialEnergy=True,
temperature=True,
totalEnergy=True))
simulation.reporters.append(
app.CheckpointReporter('checkpnt.chk', report_freq))
if check_point:
simulation.loadCheckpoint(check_point)
nsteps = int(sim_time / dt)
simulation.step(nsteps)
def openmm_simulate_amber_fs_pep(pdb_file,
top_file=None,
check_point=None,
GPU_index=0,
output_traj="output.dcd",
output_log="output.log",
output_cm=None,
report_time=10 * u.picoseconds,
sim_time=10 * u.nanoseconds):
"""
Start and run an OpenMM implicit solvent simulation with Langevin integrator at 2 fs
time step and 300 K. The cutoff distance for nonbonded interactions were
set at 1.2 nm and LJ switch distance at 1.0 nm. Long-range nonbonded
interactions were handled with PME.
Set up was referring to http://https://figshare.com/articles/Fs_MD_Trajectories/1030363
Parameters
----------
pdb_file : coordinates file (.gro, .pdb, ...)
This is the molecule configuration file contains all the atom position
and PBC (periodic boundary condition) box in the system.
check_point : None or check point file to load
GPU_index : Int or Str
The device # of GPU to use for running the simulation. Use Strings, '0,1'
for example, to use more than 1 GPU
output_traj : the trajectory file (.dcd)
This is the file stores all the coordinates information of the MD
simulation results.
output_log : the log file (.log)
This file stores the MD simulation status, such as steps, time, potential
energy, temperature, speed, etc.
output_cm : the h5 file contains contact map information
report_time : 10 ps
The program writes its information to the output every 10 ps by default
sim_time : 10 ns
The timespan of the simulation trajectory
"""
if top_file:
pdb = pmd.load_file(top_file, xyz=pdb_file)
system = pdb.createSystem(nonbondedMethod=app.CutoffNonPeriodic,
nonbondedCutoff=1.0 * u.nanometer,
constraints=app.HBonds,
implicitSolvent=app.OBC1)
else:
pdb = pmd.load_file(pdb_file)
forcefield = app.ForceField('amber99sbildn.xml', 'amber99_obc.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=app.CutoffNonPeriodic,
nonbondedCutoff=1.0 * u.nanometer,
constraints=app.HBonds)
dt = 0.002 * u.picoseconds
integrator = omm.LangevinIntegrator(300 * u.kelvin, 91.0 / u.picosecond,
dt)
integrator.setConstraintTolerance(0.00001)
try:
platform = omm.Platform_getPlatformByName("CUDA")
properties = {'DeviceIndex': str(GPU_index), 'CudaPrecision': 'mixed'}
except Exception:
platform = omm.Platform_getPlatformByName("OpenCL")
properties = {'DeviceIndex': str(GPU_index)}
simulation = app.Simulation(pdb.topology, system, integrator, platform,
properties)
simulation.context.setPositions(random.choice(pdb.get_coordinates()) /
10) #parmed \AA to OpenMM nm
# equilibrate
simulation.minimizeEnergy()
simulation.context.setVelocitiesToTemperature(300 * u.kelvin,
random.randint(1, 10000))
simulation.step(int(100 * u.picoseconds / (2 * u.femtoseconds)))
report_freq = int(report_time / dt)
simulation.reporters.append(app.DCDReporter(output_traj, report_freq))
if output_cm:
simulation.reporters.append(ContactMapReporter(output_cm, report_freq))
simulation.reporters.append(
app.StateDataReporter(output_log,
report_freq,
step=True,
time=True,
speed=True,
potentialEnergy=True,
temperature=True,
totalEnergy=True))
simulation.reporters.append(
app.CheckpointReporter('checkpnt.chk', report_freq))
if check_point:
simulation.loadCheckpoint(check_point)
nsteps = int(sim_time / dt)
simulation.step(nsteps)