def executeFarForceTest(OuterForceType, adjustment):
rswitch_inner = 6.5 * unit.angstroms
rcut_inner = 7.0 * unit.angstroms
rswitch = 9.5 * unit.angstroms
rcut = 10 * unit.angstroms
case = 'tests/data/q-SPC-FW'
pdb = app.PDBFile(case + '.pdb')
forcefield = app.ForceField(case + '.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=openmm.app.PME)
nbforce = atomsmm.hijackForce(system, atomsmm.findNonbondedForce(system))
innerforce = atomsmm.NearNonbondedForce(rcut_inner, rswitch_inner,
adjustment)
innerforce.importFrom(nbforce).addTo(system)
outerforce = OuterForceType(innerforce, rcut, rswitch).setForceGroup(2)
outerforce.importFrom(nbforce).addTo(system)
potential = atomsmm.splitPotentialEnergy(system, pdb.topology,
pdb.positions)["Total"]
refsys = forcefield.createSystem(pdb.topology,
nonbondedMethod=openmm.app.PME,
nonbondedCutoff=rcut,
removeCMMotion=True)
force = refsys.getForce(refsys.getNumForces() - 2)
force.setUseSwitchingFunction(True)
force.setSwitchingDistance(rswitch)
refpot = atomsmm.splitPotentialEnergy(refsys, pdb.topology,
pdb.positions)["Total"]
assert potential / potential.unit == pytest.approx(refpot / refpot.unit)
def execute(shifted):
rswitch_inner = 6.5*unit.angstroms
rcut_inner = 7.0*unit.angstroms
rswitch = 9.5*unit.angstroms
rcut = 10*unit.angstroms
case = 'tests/data/q-SPC-FW'
pdb = app.PDBFile(case + '.pdb')
forcefield = app.ForceField(case + '.xml')
system = forcefield.createSystem(pdb.topology)
nbforce = atomsmm.hijackForce(system, atomsmm.findNonbondedForce(system))
exceptions = atomsmm.NonbondedExceptionsForce()
exceptions.importFrom(nbforce).addTo(system)
innerforce = atomsmm.NearNonbondedForce(rcut_inner, rswitch_inner, shifted).setForceGroup(1)
innerforce.importFrom(nbforce).addTo(system)
outerforce = atomsmm.FarNonbondedForce(innerforce, rcut, rswitch).setForceGroup(2)
outerforce.importFrom(nbforce).addTo(system)
potential = atomsmm.splitPotentialEnergy(system, pdb.topology, pdb.positions)
refsys = forcefield.createSystem(pdb.topology,
nonbondedMethod=openmm.app.PME,
nonbondedCutoff=rcut,
removeCMMotion=True)
force = refsys.getForce(refsys.getNumForces()-2)
force.setUseSwitchingFunction(True)
force.setSwitchingDistance(rswitch)
refpot = atomsmm.splitPotentialEnergy(refsys, pdb.topology, pdb.positions)
E = potential["Total"]
refE = refpot["Total"]
assert E/E.unit == pytest.approx(refE/refE.unit)
E = potential["CustomBondForce"] + potential["NonbondedForce"]
refE = refpot["NonbondedForce"]
assert E/E.unit == pytest.approx(refE/refE.unit)
def executeNearForceTest(adjustment, target):
rcut = 10 * unit.angstroms
rswitch = 9.5 * unit.angstroms
case = 'tests/data/q-SPC-FW'
pdb = app.PDBFile(case + '.pdb')
forcefield = app.ForceField(case + '.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=app.CutoffPeriodic)
force = atomsmm.NearNonbondedForce(rcut, rswitch, adjustment)
force.importFrom(
atomsmm.hijackForce(system,
atomsmm.findNonbondedForce(system))).addTo(system)
integrator = openmm.VerletIntegrator(0.0 * unit.femtoseconds)
platform = openmm.Platform.getPlatformByName('Reference')
simulation = app.Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions)
state = simulation.context.getState(getEnergy=True)
potential = state.getPotentialEnergy()
assert potential / potential.unit == pytest.approx(target)
# case = 'q-SPC-FW'
case = 'emim_BCN4_Jiung2014'
pdb = app.PDBFile('../../tests/data/%s.pdb' % case)
forcefield = app.ForceField('../../tests/data/%s.xml' % case)
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=openmm.app.PME,
nonbondedCutoff=rcut,
rigidWater=False)
nbforceIndex = atomsmm.findNonbondedForce(system)
dof = atomsmm.countDegreesOfFreedom(system)
if mts:
nbforce = atomsmm.hijackForce(system, nbforceIndex)
exceptions = atomsmm.NonbondedExceptionsForce().setForceGroup(0)
innerForce = atomsmm.NearNonbondedForce(rcutIn, rswitchIn,
shift).setForceGroup(1)
outerForce = atomsmm.FarNonbondedForce(innerForce, rcut,
rswitch).setForceGroup(2)
for force in [exceptions, innerForce, outerForce]:
force.importFrom(nbforce)
force.addTo(system)
NVE = atomsmm.RespaPropagator([2, 2, 1])
integrator = atomsmm.GlobalThermostatIntegrator(dt, NVE)
else:
nbforce = system.getForce(nbforceIndex)
nbforce.setUseSwitchingFunction(True)
nbforce.setSwitchingDistance(rswitch)
# thermostat = atomsmm.VelocityRescalingPropagator(temp, dof, 1/friction)
thermostat = atomsmm.NoseHooverLangevinPropagator(temp, dof, 1 / friction,
friction)
NVE = atomsmm.VelocityVerletPropagator()