def setUp():
global topology, template, system, nan_causing_template
template = peng.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
topology = peng.to_openmm_topology(template)
# Generated using OpenMM Script Builder
# http://builder.openmm.org
forcefield = app.ForceField(
'amber96.xml', # solute FF
'tip3p.xml' # solvent FF
)
# OpenMM System
system = forcefield.createSystem(
topology,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0*u.nanometers,
constraints=app.HBonds,
ewaldErrorTolerance=0.0005
)
# this is crude but does the trick
nan_causing_template = template.copy()
kinetics = template.kinetics.copy()
# this is crude but does the trick
kinetics.velocities = kinetics.velocities.copy()
kinetics.velocities[0] = \
(np.zeros(template.velocities.shape[1]) + 1000000.) * \
u.nanometers / u.picoseconds
nan_causing_template.kinetics = kinetics
def setup_module():
global topology, template, system, nan_causing_template
if not (u and mm and app and md):
raise SkipTest
template = peng.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
topology = peng.to_openmm_topology(template)
# Generated using OpenMM Script Builder
# http://builder.openmm.org
forcefield = app.ForceField(
'amber96.xml', # solute FF
'tip3p.xml' # solvent FF
)
# OpenMM System
system = forcefield.createSystem(
topology,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0*u.nanometers,
constraints=app.HBonds,
ewaldErrorTolerance=0.0005
)
# this is crude but does the trick
nan_causing_template = template.copy()
kinetics = template.kinetics.copy()
# this is crude but does the trick
kinetics.velocities = kinetics.velocities.copy()
kinetics.velocities[0] = \
(np.zeros(template.velocities.shape[1]) + 1000000.) * \
u.nanometers / u.picoseconds
nan_causing_template.kinetics = kinetics
def run_steps(steps):
template = peng.snapshot_from_pdb(
"/Users/jan-hendrikprinz/Studium/git/openpathsampling/examples/data/Alanine_solvated.pdb")
topology = peng.to_openmm_topology(template)
# Generated using OpenMM Script Builder
# http://builder.openmm.org
forcefield = mm.app.ForceField(
'amber96.xml', # solute FF
'tip3p.xml' # solvent FF
)
# OpenMM System
system = forcefield.createSystem(
topology,
nonbondedMethod=mm.app.PME,
nonbondedCutoff=1.0*u.nanometers,
constraints=mm.app.HBonds,
ewaldErrorTolerance=0.0005
)
# OpenMM Integrator
integrator = mm.LangevinIntegrator(
300 * u.kelvin,
1.0 / u.picoseconds,
2.0 * u.femtoseconds
)
integrator.setConstraintTolerance(0.00001)
# Engine options
options = {
'n_steps_per_frame': 2,
'n_frames_max': 5
}
engine = peng.Engine(
template.topology,
system,
integrator,
options=options
)
engine.initialize('CPU')
traj = engine.generate(template, paths.LengthEnsemble(steps).can_append)
return traj