def test_BussiThermostat():
system, positions, topology = readSystem('emim_BCN4_Jiung2014')
dof = atomsmm.countDegreesOfFreedom(system)
NVE = atomsmm.VelocityVerletPropagator()
thermostat = atomsmm.VelocityRescalingPropagator(300*unit.kelvin, dof, 0.1*unit.picoseconds)
integrator = atomsmm.GlobalThermostatIntegrator(1*unit.femtoseconds, NVE, thermostat, 1)
execute(integrator, -13064.351037463852)
def test_Chained():
system, positions, topology = readSystem('emim_BCN4_Jiung2014')
dof = atomsmm.countDegreesOfFreedom(system)
NVE = atomsmm.VelocityVerletPropagator()
thermostat = atomsmm.VelocityRescalingPropagator(300*unit.kelvin, dof, 0.1*unit.picoseconds)
integrator = atomsmm.ChainedPropagator(NVE, thermostat).integrator(1*unit.femtoseconds)
integrator.setRandomNumberSeed(1)
execute(integrator, -13064.756951334914)
def test_TrotterSuzuki():
system, positions, topology = readSystem('emim_BCN4_Jiung2014')
dof = atomsmm.countDegreesOfFreedom(system)
NVE = atomsmm.VelocityVerletPropagator()
thermostat = atomsmm.VelocityRescalingPropagator(300*unit.kelvin, dof, 0.1*unit.picoseconds)
combined = atomsmm.TrotterSuzukiPropagator(NVE, thermostat)
integrator = combined.integrator(1*unit.femtoseconds)
integrator.setRandomNumberSeed(1)
execute(integrator, -13064.351037463852)
def test_NoseHooverPropagator():
system, positions, topology = readSystem('emim_BCN4_Jiung2014')
dof = atomsmm.countDegreesOfFreedom(system)
NVE = atomsmm.VelocityVerletPropagator()
thermostat = atomsmm.NoseHooverPropagator(300*unit.kelvin, dof, 10*unit.femtoseconds, 2)
thermostat = atomsmm.SuzukiYoshidaPropagator(thermostat, 3)
combined = atomsmm.TrotterSuzukiPropagator(NVE, thermostat)
integrator = combined.integrator(1*unit.femtoseconds)
integrator.setRandomNumberSeed(1)
execute(integrator, -13067.685398497035)
shift = True
mts = False
# mts = True
# 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)
