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)
def test_VelocityVerlet():
NVE = atomsmm.VelocityVerletPropagator()
integrator = atomsmm.GlobalThermostatIntegrator(1*unit.femtoseconds, NVE)
execute(integrator, -13069.385589639898)
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()
integrator = atomsmm.TrotterSuzukiPropagator(NVE,
thermostat).integrator(dt)
integrator.setRandomNumberSeed(seed)
integrator.pretty_print()
for (term,
energy) in atomsmm.utils.splitPotentialEnergy(system, pdb.topology,
pdb.positions).items():
print(term + ":", energy)
platform = openmm.Platform.getPlatformByName('CUDA')
properties = {"Precision": "mixed"}
simulation = app.Simulation(pdb.topology, system, integrator, platform,
properties)