# Create test system
from collections import namedtuple
LocalTestSystem = namedtuple('LocalTestSystem',
['name', 'system', 'topology', 'positions'])
testsystem = LocalTestSystem(name='CB7:B2',
system=system,
topology=topology,
positions=positions)
# Generate an OpenPathSampling template.
print('Creating template...')
template = engine.snapshot_from_testsystem(testsystem)
print('Creating an integrator...')
integrator = VVVRIntegrator(temperature, collision_rate, timestep)
integrator.setConstraintTolerance(1.0e-6)
print("Selecting a platform...")
platform_name = 'CUDA'
platform = openmm.Platform.getPlatformByName(platform_name)
openmm_properties = {'OpenCLPrecision': 'mixed'}
# Create an engine
print('Creating engine...')
engine_options = {
'n_frames_max': 1000,
'platform': platform_name,
'n_steps_per_frame': 50
}
engine = engine.Engine(template.topology,
system,
del context, integrator, system_with_barostat
else:
print('System does not use periodic boundary conditions; skipping equilibration.')
# Create test system
from collections import namedtuple
LocalTestSystem = namedtuple('LocalTestSystem', ['name', 'system', 'topology', 'positions'])
testsystem = LocalTestSystem(name='CB7:B2', system=system, topology=topology, positions=positions)
# Generate an OpenPathSampling template.
print('Creating template...')
template = engine.snapshot_from_testsystem(testsystem)
print('Creating an integrator...')
integrator = VVVRIntegrator(temperature, collision_rate, timestep)
integrator.setConstraintTolerance(1.0e-6)
print("Selecting a platform...")
platform_name = 'CUDA'
platform = openmm.Platform.getPlatformByName(platform_name)
openmm_properties = {'OpenCLPrecision': 'mixed'}
# Create an engine
print('Creating engine...')
engine_options = {
'n_frames_max': 1000,
'platform': platform_name,
'n_steps_per_frame': 50
}
engine = engine.Engine(
template.topology,
# 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
}
