def runOneTest(testName, options):
"""Perform a single benchmarking simulation."""
explicit = (testName in ('rf', 'pme', 'amoebapme'))
amoeba = (testName in ('amoebagk', 'amoebapme'))
apoa1 = testName.startswith('apoa1')
hydrogenMass = None
print()
if amoeba:
print('Test: %s (epsilon=%g)' % (testName, options.epsilon))
elif testName == 'pme':
print('Test: pme (cutoff=%g)' % options.cutoff)
else:
print('Test: %s' % testName)
platform = mm.Platform.getPlatformByName(options.platform)
# Create the System.
if amoeba:
constraints = None
epsilon = float(options.epsilon)
if explicit:
ff = app.ForceField('amoeba2009.xml')
pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
cutoff = 0.7 * unit.nanometers
vdwCutoff = 0.9 * unit.nanometers
system = ff.createSystem(pdb.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=cutoff,
vdwCutoff=vdwCutoff,
constraints=constraints,
ewaldErrorTolerance=0.00075,
mutualInducedTargetEpsilon=epsilon,
polarization=options.polarization)
else:
ff = app.ForceField('amoeba2009.xml', 'amoeba2009_gk.xml')
pdb = app.PDBFile('5dfr_minimized.pdb')
cutoff = 2.0 * unit.nanometers
vdwCutoff = 1.2 * unit.nanometers
system = ff.createSystem(pdb.topology,
nonbondedMethod=app.NoCutoff,
constraints=constraints,
mutualInducedTargetEpsilon=epsilon,
polarization=options.polarization)
for f in system.getForces():
if isinstance(f, mm.AmoebaMultipoleForce) or isinstance(
f, mm.AmoebaVdwForce) or isinstance(
f, mm.AmoebaGeneralizedKirkwoodForce) or isinstance(
f, mm.AmoebaWcaDispersionForce):
f.setForceGroup(1)
dt = 0.002 * unit.picoseconds
integ = mm.MTSIntegrator(dt, [(0, 2), (1, 1)])
else:
if apoa1:
ff = app.ForceField('amber14/protein.ff14SB.xml',
'amber14/lipid17.xml', 'amber14/tip3p.xml')
pdb = app.PDBFile('apoa1.pdb')
if testName == 'apoa1pme':
method = app.PME
cutoff = options.cutoff
elif testName == 'apoa1ljpme':
method = app.LJPME
cutoff = options.cutoff
else:
method = app.CutoffPeriodic
cutoff = 1 * unit.nanometers
friction = 1 * (1 / unit.picoseconds)
hydrogenMass = 1.5 * unit.amu
elif explicit:
ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
if testName == 'pme':
method = app.PME
cutoff = options.cutoff
else:
method = app.CutoffPeriodic
cutoff = 1 * unit.nanometers
friction = 1 * (1 / unit.picoseconds)
else:
ff = app.ForceField('amber99sb.xml', 'amber99_obc.xml')
pdb = app.PDBFile('5dfr_minimized.pdb')
method = app.CutoffNonPeriodic
cutoff = 2 * unit.nanometers
friction = 91 * (1 / unit.picoseconds)
if options.heavy:
dt = 0.005 * unit.picoseconds
constraints = app.AllBonds
hydrogenMass = 4 * unit.amu
integ = mm.LangevinIntegrator(300 * unit.kelvin, friction, dt)
else:
dt = 0.004 * unit.picoseconds
constraints = app.HBonds
integ = mm.LangevinMiddleIntegrator(300 * unit.kelvin, friction,
dt)
system = ff.createSystem(pdb.topology,
nonbondedMethod=method,
nonbondedCutoff=cutoff,
constraints=constraints,
hydrogenMass=hydrogenMass)
print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
properties = {}
initialSteps = 5
if options.device is not None and platform.getName() in ('CUDA', 'OpenCL'):
properties['DeviceIndex'] = options.device
if ',' in options.device or ' ' in options.device:
initialSteps = 250
if options.precision is not None and platform.getName() in ('CUDA',
'OpenCL'):
properties['Precision'] = options.precision
# Run the simulation.
integ.setConstraintTolerance(1e-5)
if len(properties) > 0:
context = mm.Context(system, integ, platform, properties)
else:
context = mm.Context(system, integ, platform)
context.setPositions(pdb.positions)
context.setVelocitiesToTemperature(300 * unit.kelvin)
steps = 20
while True:
time = timeIntegration(context, steps, initialSteps)
if time >= 0.5 * options.seconds:
break
if time < 0.5:
steps = int(
steps * 1.0 / time
) # Integrate enough steps to get a reasonable estimate for how many we'll need.
else:
steps = int(steps * options.seconds / time)
print('Integrated %d steps in %g seconds' % (steps, time))
print('%g ns/day' %
(dt * steps * 86400 / time).value_in_unit(unit.nanoseconds))
platform = mm.Platform.getPlatformByName('CUDA')
properties = {'CudaPrecision': "single"}
temperature = 1 * u.kelvin
timestep = 1.0 * u.femtoseconds
steps = 5000
#hmc_integrators.guess_force_groups(system, nonbonded=0, others=1, fft=0)
#groups = [(0, 1), (1, 4)]
hmc_integrators.guess_force_groups(system, nonbonded=0, others=0, fft=0)
groups = [(0, 1)]
integrator = mm.MTSIntegrator(timestep, groups)
simulation = app.Simulation(topology, system, integrator, platform=platform, platformProperties=properties)
simulation.context.setPositions(positions)
simulation.context.setVelocitiesToTemperature(temperature)
integrator.step(1)
t0 = time.time()
integrator.step(steps)
dt = time.time() - t0
outer_per_day = steps / dt * 60 * 60 * 24
outer_per_sec = steps / dt
inner_per_sec = outer_per_sec * groups[-1][1]
ns_per_day = (timestep / u.nanoseconds) * outer_per_day
for force in system.getForces():
if isinstance(force, slow):
found_slow = True
force.setForceGroup(1)
else:
force.setForceGroup(0)
if not found_slow:
raise ValueError('No slow AMOEBA forces found for MTS integrator!')
# The list given to MTSIntegrator defining the time steps and force
# decompositions is a list of 2-element tuples where the first element is
# a force group and the second element is how many times to evaluate that
# force group each "outer" time-step. So [(0, opt.nrespa), (1, 1)] means
# force group 0 is executed nrespa times each time step and force group 1 is
# executed only once. The slow forces are defined above as force group 1 and
# all others as force group 0.
integrator = mm.MTSIntegrator(opt.timestep*u.femtoseconds,
[(0, opt.nrespa), (1, 1)])
print('RESPA MTS Integrator: %8.2f fs outer time-step with %d inner steps' %
(opt.timestep, opt.nrespa))
else:
integrator = mm.VerletIntegrator(opt.timestep*u.femtoseconds)
print('Verlet: %8.2f fs' % opt.timestep )
sim = app.Simulation(pdb.topology, system, integrator,
mm.Platform.getPlatformByName('CUDA'),
dict(CudaPrecision='mixed') )
if opt.hawkeye:
# Watch every step... slow!
sim.reporters.append(ErrorDetectionReporter(groups_and_names))
sim.reporters.append(
pmd.openmm.StateDataReporter(opt.output, reportInterval=opt.interval,
steps=equil_steps,
minimize=True,
use_hmc=False,
precision=precision,
platform_name=platform_name)
n_iter = 1000
n_steps = 25
temperature = 300. * u.kelvin
timestep = 1.0 * u.femtoseconds
x = []
integrators = [
mm.VerletIntegrator(timestep), # 0
mm.MTSIntegrator(timestep, groups=((0, 1), (1, 1))), # 1
mm.MTSIntegrator(timestep, groups=((0, 2), (1, 1))), # 2
mm.MTSIntegrator(timestep, groups=((0, 3), (1, 1))), # 3
mm.MTSIntegrator(timestep, groups=((0, 4), (1, 1))), # 4
mm.MTSIntegrator(timestep, groups=((0, 5), (1, 1))), # 5
mm.MTSIntegrator(timestep, groups=((1, 1), (0, 1))), # 6
mm.MTSIntegrator(timestep, groups=((1, 3), (0, 1))), # 7
mm.MTSIntegrator(timestep, groups=((1, 2), (0, 1))), # 8
mm.MTSIntegrator(timestep, groups=((1, 4), (0, 1))), # 9
mm.MTSIntegrator(timestep, groups=((1, 5), (0, 1))), # 10
]
for (i, integrator) in enumerate(integrators):
print("*" * 80)
simulation = lb_loader.build(testsystem,
integrator,
temperature,
def runOneTest(testName, options):
"""Perform a single benchmarking simulation."""
explicit = (testName not in ('gbsa', 'amoebagk'))
amoeba = (testName in ('amoebagk', 'amoebapme'))
apoa1 = testName.startswith('apoa1')
amber = (testName.startswith('amber'))
hydrogenMass = None
print()
if amoeba:
print('Test: %s (epsilon=%g)' % (testName, options.epsilon))
elif testName == 'pme':
print('Test: pme (cutoff=%g)' % options.cutoff)
else:
print('Test: %s' % testName)
print('Ensemble: %s' % options.ensemble)
platform = mm.Platform.getPlatformByName(options.platform)
# Create the System.
temperature = 300 * unit.kelvin
if explicit:
friction = 1 * (1 / unit.picoseconds)
else:
friction = 91 * (1 / unit.picoseconds)
if amoeba:
constraints = None
epsilon = float(options.epsilon)
if explicit:
ff = app.ForceField('amoeba2009.xml')
pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
cutoff = 0.7 * unit.nanometers
vdwCutoff = 0.9 * unit.nanometers
system = ff.createSystem(pdb.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=cutoff,
vdwCutoff=vdwCutoff,
constraints=constraints,
ewaldErrorTolerance=0.00075,
mutualInducedTargetEpsilon=epsilon,
polarization=options.polarization)
else:
ff = app.ForceField('amoeba2009.xml', 'amoeba2009_gk.xml')
pdb = app.PDBFile('5dfr_minimized.pdb')
cutoff = 2.0 * unit.nanometers
vdwCutoff = 1.2 * unit.nanometers
system = ff.createSystem(pdb.topology,
nonbondedMethod=app.NoCutoff,
constraints=constraints,
mutualInducedTargetEpsilon=epsilon,
polarization=options.polarization)
for f in system.getForces():
if isinstance(f, mm.AmoebaMultipoleForce) or isinstance(
f, mm.AmoebaVdwForce) or isinstance(
f, mm.AmoebaGeneralizedKirkwoodForce) or isinstance(
f, mm.AmoebaWcaDispersionForce):
f.setForceGroup(1)
dt = 0.002 * unit.picoseconds
if options.ensemble == 'NVE':
integ = mm.MTSIntegrator(dt, [(0, 2), (1, 1)])
else:
integ = mm.MTSLangevinIntegrator(temperature, friction, dt,
[(0, 2), (1, 1)])
positions = pdb.positions
elif amber:
dirname = downloadAmberSuite()
names = {
'amber20-dhfr': 'JAC',
'amber20-factorix': 'FactorIX',
'amber20-cellulose': 'Cellulose',
'amber20-stmv': 'STMV'
}
fileName = names[testName]
prmtop = app.AmberPrmtopFile(
os.path.join(dirname, f'PME/Topologies/{fileName}.prmtop'))
inpcrd = app.AmberInpcrdFile(
os.path.join(dirname, f'PME/Coordinates/{fileName}.inpcrd'))
topology = prmtop.topology
positions = inpcrd.positions
dt = 0.004 * unit.picoseconds
method = app.PME
cutoff = options.cutoff
constraints = app.HBonds
system = prmtop.createSystem(nonbondedMethod=method,
nonbondedCutoff=cutoff,
constraints=constraints)
if options.ensemble == 'NVE':
integ = mm.VerletIntegrator(dt)
else:
integ = mm.LangevinMiddleIntegrator(temperature, friction, dt)
else:
if apoa1:
ff = app.ForceField('amber14/protein.ff14SB.xml',
'amber14/lipid17.xml', 'amber14/tip3p.xml')
pdb = app.PDBFile('apoa1.pdb')
if testName == 'apoa1pme':
method = app.PME
cutoff = options.cutoff
elif testName == 'apoa1ljpme':
method = app.LJPME
cutoff = options.cutoff
else:
method = app.CutoffPeriodic
cutoff = 1 * unit.nanometers
hydrogenMass = 1.5 * unit.amu
elif explicit:
ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
if testName == 'pme':
method = app.PME
cutoff = options.cutoff
else:
method = app.CutoffPeriodic
cutoff = 1 * unit.nanometers
else:
ff = app.ForceField('amber99sb.xml', 'amber99_obc.xml')
pdb = app.PDBFile('5dfr_minimized.pdb')
method = app.CutoffNonPeriodic
cutoff = 2 * unit.nanometers
if options.heavy:
dt = 0.005 * unit.picoseconds
constraints = app.AllBonds
hydrogenMass = 4 * unit.amu
if options.ensemble == 'NVE':
integ = mm.VerletIntegrator(dt)
else:
integ = mm.LangevinIntegrator(temperature, friction, dt)
else:
dt = 0.004 * unit.picoseconds
constraints = app.HBonds
if options.ensemble == 'NVE':
integ = mm.VerletIntegrator(dt)
else:
integ = mm.LangevinMiddleIntegrator(temperature, friction, dt)
positions = pdb.positions
system = ff.createSystem(pdb.topology,
nonbondedMethod=method,
nonbondedCutoff=cutoff,
constraints=constraints,
hydrogenMass=hydrogenMass)
if options.ensemble == 'NPT':
system.addForce(mm.MonteCarloBarostat(1 * unit.bar, temperature, 100))
print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
properties = {}
initialSteps = 5
if options.device is not None and platform.getName() in ('CUDA', 'OpenCL'):
properties['DeviceIndex'] = options.device
if ',' in options.device or ' ' in options.device:
initialSteps = 250
if options.precision is not None and platform.getName() in ('CUDA',
'OpenCL'):
properties['Precision'] = options.precision
# Run the simulation.
integ.setConstraintTolerance(1e-5)
if len(properties) > 0:
context = mm.Context(system, integ, platform, properties)
else:
context = mm.Context(system, integ, platform)
context.setPositions(positions)
if amber:
if inpcrd.boxVectors is not None:
context.setPeriodicBoxVectors(*inpcrd.boxVectors)
mm.LocalEnergyMinimizer.minimize(
context, 100 * unit.kilojoules_per_mole / unit.nanometer)
context.setVelocitiesToTemperature(temperature)
steps = 20
while True:
time = timeIntegration(context, steps, initialSteps)
if time >= 0.5 * options.seconds:
break
if time < 0.5:
steps = int(
steps * 1.0 / time
) # Integrate enough steps to get a reasonable estimate for how many we'll need.
else:
steps = int(steps * options.seconds / time)
print('Integrated %d steps in %g seconds' % (steps, time))
print('%g ns/day' %
(dt * steps * 86400 / time).value_in_unit(unit.nanoseconds))
def runOneTest(testName, options):
"""Perform a single benchmarking simulation."""
explicit = (testName in ('rf', 'pme', 'amoebapme'))
amoeba = (testName in ('amoebagk', 'amoebapme'))
hydrogenMass = None
print()
if amoeba:
print('Test: %s (epsilon=%g)' % (testName, options.epsilon))
elif testName == 'pme':
print('Test: pme (cutoff=%g)' % options.cutoff)
else:
print('Test: %s' % testName)
platform = mm.Platform.getPlatformByName(options.platform)
# Create the System.
if amoeba:
constraints = None
epsilon = float(options.epsilon)
if explicit:
ff = app.ForceField('amoeba2009.xml')
pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
cutoff = 0.7*unit.nanometers
vdwCutoff = 0.9*unit.nanometers
system = ff.createSystem(pdb.topology, nonbondedMethod=app.PME, nonbondedCutoff=cutoff, vdwCutoff=vdwCutoff, constraints=constraints, ewaldErrorTolerance=0.00075, mutualInducedTargetEpsilon=epsilon, polarization=options.polarization)
else:
ff = app.ForceField('amoeba2009.xml', 'amoeba2009_gk.xml')
pdb = app.PDBFile('5dfr_minimized.pdb')
cutoff = 2.0*unit.nanometers
vdwCutoff = 1.2*unit.nanometers
system = ff.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=constraints, mutualInducedTargetEpsilon=epsilon, polarization=options.polarization)
for f in system.getForces():
if isinstance(f, mm.AmoebaMultipoleForce) or isinstance(f, mm.AmoebaVdwForce) or isinstance(f, mm.AmoebaGeneralizedKirkwoodForce) or isinstance(f, mm.AmoebaWcaDispersionForce):
f.setForceGroup(1)
dt = 0.002*unit.picoseconds
if options.timestep:
dt = options.timestep * unit.femtoseconds
integ = mm.MTSIntegrator(dt, [(0,2), (1,1)])
else:
if explicit:
ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
if testName == 'pme':
method = app.PME
cutoff = options.cutoff
else:
method = app.CutoffPeriodic
cutoff = 1*unit.nanometers
else:
ff = app.ForceField('amber99sb.xml', 'amber99_obc.xml')
pdb = app.PDBFile('5dfr_minimized.pdb')
method = app.CutoffNonPeriodic
cutoff = 2*unit.nanometers
if options.heavy:
dt = 0.005*unit.picoseconds
if options.timestep:
dt = options.timestep * unit.femtoseconds
constraints = app.AllBonds
hydrogenMass = 4*unit.amu
else:
dt = 0.002*unit.picoseconds
if options.timestep:
dt = options.timestep * unit.femtoseconds
constraints = app.HBonds
hydrogenMass = None
system = ff.createSystem(pdb.topology, nonbondedMethod=method, nonbondedCutoff=cutoff, constraints=constraints, hydrogenMass=hydrogenMass)
integ = mm.LangevinIntegrator(300*unit.kelvin, 91*(1/unit.picoseconds), dt)
print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
properties = {}
initialSteps = 5
if options.device is not None and platform.getName() in ('CUDA', 'OpenCL'):
properties['DeviceIndex'] = options.device
if ',' in options.device or ' ' in options.device:
initialSteps = 250
if options.precision is not None and platform.getName() in ('CUDA', 'OpenCL'):
properties['CudaPrecision'] = options.precision
# Use switching function
switch_width = 2.0 * unit.angstroms
for force in system.getForces():
if isinstance(force, mm.NonbondedForce):
force.setUseSwitchingFunction(True)
cutoff = force.getCutoffDistance()
force.setSwitchingDistance(cutoff - switch_width)
force.setReactionFieldDielectric(1e10)
force.setEwaldErrorTolerance(1.0e-7)
# Run the simulation.
integ.setConstraintTolerance(1e-8)
if len(properties) > 0:
context = mm.Context(system, integ, platform, properties)
else:
context = mm.Context(system, integ, platform)
context.setPositions(pdb.positions)
context.setVelocitiesToTemperature(300*unit.kelvin)
steps = 20
while True:
time = timeIntegration(context, steps, initialSteps)
if time >= 0.5*options.seconds:
break
if time < 0.5:
steps = int(steps*1.0/time) # Integrate enough steps to get a reasonable estimate for how many we'll need.
else:
steps = int(steps*options.seconds/time)
print('Integrated %d steps in %g seconds' % (steps, time))
print('%g ns/day' % (dt*steps*86400/time).value_in_unit(unit.nanoseconds))
if options.drift is not None:
print('Measuring drift with Verlet integrator')
state = context.getState(getPositions=True, getVelocities=True)
positions = state.getPositions()
velocities = state.getVelocities()
box_vectors = state.getPeriodicBoxVectors()
del context, integ
integ = mm.VerletIntegrator(dt)
print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
initialSteps = 500
integ.setConstraintTolerance(1e-8)
print('Integrator tolerance: %f' % integ.getConstraintTolerance())
if len(properties) > 0:
context = mm.Context(system, integ, platform, properties)
else:
context = mm.Context(system, integ, platform)
context.setPeriodicBoxVectors(*box_vectors)
context.setPositions(positions)
context.setVelocities(velocities)
measureDrift(context, steps, initialSteps, filename=options.drift, name=options.test)
def run_benchmark(test_name, options, stream=None):
"""Perform a single benchmarking simulation."""
if stream is None:
stream = sys.stdout
benchmark_data_dir = os.path.join(os.path.dirname(__file__), "data")
explicit = any([x in test_name for x in ["rf", "pme", "amoebapme"]])
amoeba = any([x in test_name for x in ["amoebagk", "amoebapme"]])
hydrogenMass = None
if amoeba:
stream.write('Test: %s (epsilon=%g)\n' % (test_name, options.amoeba_target_epsilon))
elif test_name == 'pme':
stream.write('Test: pme (cutoff=%g)\n' % options.cutoff)
else:
stream.write('Test: %s\n' % test_name)
# Create the System.
if amoeba:
constraints = None
epsilon = float(options.amoeba_target_epsilon)
if explicit:
ff = app.ForceField('amoeba2009.xml')
pdb = app.PDBFile(os.path.join(benchmark_data_dir, '5dfr_solv-cube_equil.pdb'))
cutoff = 0.7 * unit.nanometers
vdwCutoff = 0.9 * unit.nanometers
system = ff.createSystem(pdb.topology, nonbondedMethod=app.PME, nonbondedCutoff=cutoff, vdwCutoff=vdwCutoff, constraints=constraints, ewaldErrorTolerance=0.00075, mutualInducedTargetEpsilon=epsilon, polarization=options.polarization)
else:
ff = app.ForceField(
'amoeba2009.xml',
'amoeba2009_gk.xml'
)
pdb = app.PDBFile(os.path.join(benchmark_data_dir, '5dfr_minimized.pdb'))
cutoff = 2.0 * unit.nanometers
vdwCutoff = 1.2 * unit.nanometers
system = ff.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=constraints, mutualInducedTargetEpsilon=epsilon, polarization=options.polarization)
for f in system.getForces():
if isinstance(f, mm.AmoebaMultipoleForce) or isinstance(f, mm.AmoebaVdwForce) or isinstance(f, mm.AmoebaGeneralizedKirkwoodForce) or isinstance(f, mm.AmoebaWcaDispersionForce):
f.setForceGroup(1)
dt = 0.002 * unit.picoseconds
integ = mm.MTSIntegrator(dt, [(0, 2), (1, 1)])
else:
if explicit:
ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
pdb = app.PDBFile(os.path.join(benchmark_data_dir, '5dfr_solv-cube_equil.pdb'))
if 'pme' in test_name:
method = app.PME
cutoff = options.cutoff
else:
method = app.CutoffPeriodic
cutoff = 1 * unit.nanometers
friction = 1 * (1 / unit.picoseconds)
else:
ff = app.ForceField(
'amber99sb.xml',
'amber99_obc.xml'
)
pdb = app.PDBFile(os.path.join(benchmark_data_dir, '5dfr_minimized.pdb'))
method = app.CutoffNonPeriodic
cutoff = 2 * unit.nanometers
friction = 91 * (1 / unit.picoseconds)
if options.use_heavy_hydrogens:
dt = 0.005 * unit.picoseconds
constraints = app.AllBonds
hydrogenMass = 4 * unit.amu
else:
dt = 0.002 * unit.picoseconds
constraints = app.HBonds
hydrogenMass = None
system = ff.createSystem(pdb.topology, nonbondedMethod=method, nonbondedCutoff=cutoff, constraints=constraints, hydrogenMass=hydrogenMass)
integ = mm.LangevinIntegrator(300 * unit.kelvin, friction, dt)
stream.write('Step Size: %g fs\n' % dt.value_in_unit(unit.femtoseconds))
properties = {}
initialSteps = 5
if options.precision is not None and options.platform.getName() in ('CUDA', 'OpenCL'):
properties['Precision'] = options.precision
# Run the simulation.
integ.setConstraintTolerance(1e-5)
try:
if len(properties) > 0:
context = mm.Context(system, integ, options.platform, properties)
else:
context = mm.Context(system, integ, options.platform)
except Exception as e:
stream.write("Unable to Benchmark '{}'\n".format(test_name))
stream.write("ERROR: {}\n".format(str(e)))
return
context.setPositions(pdb.positions)
context.setVelocitiesToTemperature(300 * unit.kelvin)
steps = 20
while True:
time = timeIntegration(context, steps, initialSteps)
if time >= 0.5 * options.seconds:
break
if time < 0.5:
steps = int(steps * 1.0 / time) # Integrate enough steps to get a reasonable estimate for how many we'll need.
else:
steps = int(steps * options.seconds / time)
stream.write('Integrated %d steps in %g seconds\n' % (steps, time))
stream.write('%g ns/day\n' % (dt * steps * 86400 / time).value_in_unit(unit.nanoseconds))
import simtk.openmm.app as app
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import testsystems
f = lambda x: (x.getPotentialEnergy(), x.getKineticEnergy(), x.getKineticEnergy() + x.getPotentialEnergy())
temperature = 300. * u.kelvin
testsystem = testsystems.LennardJonesFluid(nparticles=2048)
timestep = 0.1 * u.femtoseconds
nsteps = 50
for platform_name in ["CUDA", "OpenCL", "CPU"]:
platform = mm.Platform.getPlatformByName(platform_name)
integrators = [mm.VerletIntegrator(timestep), mm.MTSIntegrator(timestep, groups=[(0, 1)])]
for integrator in integrators:
print(platform_name, integrator)
simulation = app.Simulation(testsystem.topology, testsystem.system, integrator, platform=platform)
simulation.context.setPositions(testsystem.positions)
simulation.context.setVelocitiesToTemperature(temperature)
integrator.step(nsteps) # Do a single step first to apply constraints before we run tests.
state1a = simulation.context.getState(getPositions=True, getParameters=True, getEnergy=True, getVelocities=True)
old = f(state1a)
print("PE, KE, TOTAL")
print(old)
integrator.step(nsteps)
state1b = simulation.context.getState(getPositions=True, getParameters=True, getEnergy=True, getVelocities=True)
new = f(state1b)
