pressure = 1.0 * unit.atmospheres
temperature = 300.0 * unit.kelvin
temperature_hot = 600.0 * unit.kelvin
frequency = 25
# If system is periodic, equilibrate at 1 atm at 300 K.
if system.usesPeriodicBoundaryConditions():
print('Equilibrating with barostat...')
import copy
barostat = openmm.MonteCarloBarostat(pressure, temperature, frequency)
system_with_barostat = copy.deepcopy(system)
system_with_barostat.addForce(barostat)
collision_rate = 10.0 / unit.picoseconds
timestep = 2.0 * unit.femtoseconds
#integrator = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
integrator = VVVRIntegrator(temperature, collision_rate, timestep)
context = openmm.Context(system_with_barostat, integrator)
context.setPositions(positions)
niterations = 20
nsteps = 500
for iteration in range(niterations):
print('Iteration %5d / %5d: volume = %8.3f nm^3' %
(iteration, niterations,
context.getState().getPeriodicBoxVolume() / unit.nanometers**3))
integrator.step(nsteps)
positions = context.getState(getPositions=True).getPositions(asNumpy=True)
box_vectors = context.getState().getPeriodicBoxVectors()
system.setDefaultPeriodicBoxVectors(*box_vectors)
del context, integrator, system_with_barostat
else:
print(
# In[2]:
# this cell is all OpenMM specific
forcefield = app.ForceField('amber96.xml', 'tip3p.xml')
pdb = app.PDBFile("AD_initial_frame.pdb")
system = forcefield.createSystem(
pdb.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0*unit.nanometers,
constraints=app.HBonds,
rigidWater=True,
ewaldErrorTolerance=0.0005
)
hi_T_integrator = VVVRIntegrator(
500*unit.kelvin,
1.0/unit.picoseconds,
2.0*unit.femtoseconds)
hi_T_integrator.setConstraintTolerance(0.00001)
# The storage file will need a template snapshot. In addition, the OPS OpenMM-based `Engine` has a few properties and options that are set by these dictionaries.
# In[3]:
template = omm.snapshot_from_pdb("AD_initial_frame.pdb")
openmm_properties = {'OpenCLPrecision': 'mixed'}
engine_options = {
'n_steps_per_frame': 10,
'n_frames_max': 2000
}
