def test_RESPASystem_with_exception_offsets():
system, positions, topology, solute = readSystem(
'hydroxyethylaminoanthraquinone-in-water')
respa_info = dict(rcutIn=7 * unit.angstroms, rswitchIn=5 * unit.angstroms)
solvation_system = atomsmm.SolvationSystem(system, solute)
nbforce = solvation_system.getForce(
atomsmm.findNonbondedForce(solvation_system))
for index in range(nbforce.getNumExceptions()):
i, j, chargeprod, sigma, epsilon = nbforce.getExceptionParameters(
index)
nbforce.setExceptionParameters(index, i, j, 0.0, sigma, epsilon)
nbforce.addExceptionParameterOffset('lambda_coul', index, chargeprod,
0.0, 0.0)
respa_system = atomsmm.RESPASystem(solvation_system, *respa_info.values())
state = dict(lambda_vdw=0.5, lambda_coul=0.5)
components = atomsmm.splitPotentialEnergy(respa_system, topology,
positions, **state)
potential = dict()
potential['HarmonicBondForce'] = 1815.1848188179738
potential['HarmonicAngleForce'] = 1111.5544374007236
potential['PeriodicTorsionForce'] = 1.5998609986459567
potential['Real-Space'] = 58201.09912379701
potential['Reciprocal-Space'] = -76436.3982762784
potential['CustomNonbondedForce'] = -64.67189605331785
potential['CustomNonbondedForce(1)'] = -17294.836032921234
potential['CustomNonbondedForce(2)'] = 17294.836032921194
potential['CustomBondForce'] = 72.25414937535754
potential['Total'] = -15299.377781942048
for term, value in components.items():
assert value / value.unit == pytest.approx(potential[term])
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 execute(integrator, target):
system, positions, topology = readSystem('emim_BCN4_Jiung2014')
nbforce = atomsmm.findNonbondedForce(system)
system.getForce(nbforce).setReciprocalSpaceForceGroup(1)
platform = openmm.Platform.getPlatformByName('Reference')
simulation = app.Simulation(topology, system, integrator, platform)
simulation.context.setPositions(positions)
simulation.context.setVelocitiesToTemperature(300*unit.kelvin, 1)
simulation.step(5)
state = simulation.context.getState(getEnergy=True)
potential = state.getPotentialEnergy()
print(potential, target)
assert potential/potential.unit == pytest.approx(target)
def __init__(self, system, atoms, group=0):
self.this = copy.deepcopy(system).this
nonbonded = self.getForce(atomsmm.findNonbondedForce(self))
potential = '4*lambda_vdw*epsilon*(1 - x)/x^2'
potential += '; x=(r/sigma)^6 + 0.5*(1 - lambda_vdw)'
potential += '; sigma = 0.5*(sigma1 + sigma2)'
potential += '; epsilon = sqrt(epsilon1*epsilon2)'
softcore = openmm.CustomNonbondedForce(potential)
if nonbonded.getNonbondedMethod() == openmm.NonbondedForce.NoCutoff:
softcore.setNonbondedMethod(openmm.CustomNonbondedForce.NoCutoff)
else:
softcore.setNonbondedMethod(
openmm.CustomNonbondedForce.CutoffPeriodic)
softcore.setCutoffDistance(nonbonded.getCutoffDistance())
softcore.setUseSwitchingFunction(nonbonded.getUseSwitchingFunction())
softcore.setSwitchingDistance(nonbonded.getSwitchingDistance())
# softcore.setUseLongRangeCorrection(nonbonded.getUseDispersionCorrection())
softcore.setUseLongRangeCorrection(False)
softcore.addGlobalParameter('lambda_vdw', 1.0)
softcore.addPerParticleParameter('sigma')
softcore.addPerParticleParameter('epsilon')
all = range(nonbonded.getNumParticles())
for index in all:
_, sigma, epsilon = nonbonded.getParticleParameters(index)
softcore.addParticle([sigma, epsilon])
softcore.addInteractionGroup(atoms, set(all) - set(atoms))
softcore.setForceGroup(group)
softcore.addEnergyParameterDerivative('lambda_vdw')
self.addForce(softcore)
parameters = []
for index in atoms:
parameters.append(nonbonded.getParticleParameters(index))
nonbonded.setParticleParameters(index, 0.0, 1.0, 0.0)
exception_pairs = []
for index in range(nonbonded.getNumExceptions()):
i, j, _, _, _ = nonbonded.getExceptionParameters(index)
if set([i, j]).issubset(atoms):
exception_pairs.append(set([i, j]))
for i, j in itertools.combinations(atoms, 2):
if set([i, j]) not in exception_pairs:
q1, sig1, eps1 = parameters[i]
q2, sig2, eps2 = parameters[j]
nonbonded.addException(i, j, q1 * q2, (sig1 + sig2) / 2,
np.sqrt(eps1 * eps2))
softcore.addExclusion(
i, j) # Needed for matching exception number
def readSystem(case):
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=10 * unit.angstroms,
rigidWater=False,
constraints=None,
removeCMMotion=False)
nbforce = system.getForce(atomsmm.findNonbondedForce(system))
nbforce.setUseSwitchingFunction(True)
nbforce.setSwitchingDistance(9 * unit.angstroms)
residues = [atom.residue.name for atom in pdb.topology.atoms()]
solute_atoms = set(i for (i, name) in enumerate(residues) if name == 'aaa')
return system, pdb.positions, pdb.topology, solute_atoms
def execute(degree, target):
rcut = 10*unit.angstroms
rswitch = 9.5*unit.angstroms
alpha = 0.29/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.DampedSmoothedForce(alpha, rcut, rswitch, degree=degree)
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)
properties = dict(Precision='mixed') if args.platform == 'CUDA' else dict()
if args.device != 'None':
properties['DeviceIndex'] = args.device
pdb = app.PDBFile(f'{base}.pdb')
residues = [atom.residue.name for atom in pdb.topology.atoms()]
solute_atoms = set(i for (i, name) in enumerate(residues) if name == 'aaa')
forcefield = app.ForceField(f'{base}.xml')
openmm_system = forcefield.createSystem(pdb.topology,
nonbondedMethod=openmm.app.PME,
nonbondedCutoff=rcut,
rigidWater=False,
removeCMMotion=False)
nbforce = openmm_system.getForce(atomsmm.findNonbondedForce(openmm_system))
nbforce.setUseSwitchingFunction(True)
nbforce.setSwitchingDistance(rswitch)
nbforce.setUseDispersionCorrection(True)
solvation_system = atomsmm.SolvationSystem(openmm_system,
solute_atoms,
use_softcore=False,
split_exceptions=False)
if args.timestep > 3:
respa_system = atomsmm.RESPASystem(solvation_system,
rcutIn,
rswitchIn,
fastExceptions=True)
loops = [6, args.timestep // 3, 1]
def __init__(self,
system,
atoms,
coupling='softcore',
group=0,
use_lrc=False):
self.this = copy.deepcopy(system).this
nonbonded = self.getForce(atomsmm.findNonbondedForce(self))
if coupling == 'softcore': # Beutler et al. (1994)
potential = 'U_softcore'
potential += '; U_softcore = 4*lambda_vdw*epsilon*(1 - x)/x^2'
potential += '; x = (r/sigma)^6 + 0.5*(1 - lambda_vdw)'
else:
if coupling in ['linear', 'spline', 'art']:
potential = 'U_{}'.format(coupling)
else:
potential = 'U_general'
potential += '; {} = 4*((gt0-gt1)*S + gt1)*epsilon*x*(x - 1)'.format(
potential)
potential += '; x = (sigma/r)^6'
potential += '; gt0 = step(lambda_vdw)'
potential += '; gt1 = step(lambda_vdw-1)'
if coupling == 'linear':
potential += '; S = lambda_vdw - sin(two_pi*lambda_vdw)/two_pi'
elif coupling == 'spline':
potential += '; S = lambda_vdw^3*(10 - 15*lambda_vdw + 6*lambda_vdw^2)'
elif coupling == 'art': # Abrams, Rosso, and Tuckerman (2006)
potential += '; S = lambda_vdw - sin(two_pi*lambda_vdw)/two_pi'
potential += '; two_pi = 6.28318530717958'
else:
potential += '; S = {}'.format(coupling)
potential += '; sigma = 0.5*(sigma1 + sigma2)'
potential += '; epsilon = sqrt(epsilon1*epsilon2)'
softcore = openmm.CustomNonbondedForce(potential)
if nonbonded.getNonbondedMethod() == openmm.NonbondedForce.NoCutoff:
softcore.setNonbondedMethod(openmm.CustomNonbondedForce.NoCutoff)
else:
softcore.setNonbondedMethod(
openmm.CustomNonbondedForce.CutoffPeriodic)
softcore.setCutoffDistance(nonbonded.getCutoffDistance())
softcore.setUseSwitchingFunction(nonbonded.getUseSwitchingFunction())
softcore.setSwitchingDistance(nonbonded.getSwitchingDistance())
# softcore.setUseLongRangeCorrection(nonbonded.getUseDispersionCorrection())
softcore.setUseLongRangeCorrection(use_lrc)
softcore.addGlobalParameter('lambda_vdw', 1.0)
softcore.addPerParticleParameter('sigma')
softcore.addPerParticleParameter('epsilon')
all_atoms = range(nonbonded.getNumParticles())
for index in all_atoms:
_, sigma, epsilon = nonbonded.getParticleParameters(index)
softcore.addParticle([sigma, epsilon])
for index in range(nonbonded.getNumExceptions()):
i, j, _, _, epsilon = nonbonded.getExceptionParameters(index)
softcore.addExclusion(i, j)
softcore.addInteractionGroup(atoms, set(all_atoms) - set(atoms))
softcore.setForceGroup(group)
softcore.addEnergyParameterDerivative('lambda_vdw')
self.addForce(softcore)
parameters = {}
for i in atoms:
parameters[i] = nonbonded.getParticleParameters(i)
nonbonded.setParticleParameters(i, 0.0, 1.0, 0.0)
exception_pairs = []
for index in range(nonbonded.getNumExceptions()):
i, j, _, _, _ = nonbonded.getExceptionParameters(index)
if set([i, j]).issubset(atoms):
exception_pairs.append(set([i, j]))
for i, j in itertools.combinations(atoms, 2):
if set([i, j]) not in exception_pairs:
q1, sig1, eps1 = parameters[i]
q2, sig2, eps2 = parameters[j]
nonbonded.addException(i, j, q1 * q2, (sig1 + sig2) / 2,
np.sqrt(eps1 * eps2))
softcore.addExclusion(
i, j) # Needed for matching exception number
def __init__(self,
system,
solute_atoms,
use_softcore=True,
softcore_group=0,
split_exceptions=False):
self.this = copy.deepcopy(system).this
nonbonded = self.getForce(atomsmm.findNonbondedForce(self))
all_atoms = set(range(nonbonded.getNumParticles()))
solvent_atoms = all_atoms - solute_atoms
# If requested, extract preexisting non-exclusion exceptions:
if split_exceptions:
ljc_potential = '4*epsilon*x*(x-1) + Kc*chargeprod/r; x=(sigma/r)^6; Kc=138.935456'
exceptions = atomsmm.forces._AtomsMM_CustomBondForce(ljc_potential)
exceptions.importFrom(nonbonded, extract=True)
if exceptions.getNumBonds() > 0:
self.addForce(exceptions)
# A custom nonbonded force for solute-solvent, softcore van der Waals interactions:
if use_softcore:
ljs_potential = '4*lambda_vdw*epsilon*(1-x)/x^2; x=(r/sigma)^6+0.5*(1-lambda_vdw)'
softcore = atomsmm.forces._AtomsMM_CustomNonbondedForce(
ljs_potential, lambda_vdw=1)
softcore.importFrom(nonbonded)
softcore.addInteractionGroup(solute_atoms, solvent_atoms)
softcore.setForceGroup(softcore_group)
self.addForce(softcore)
# All solute-solute interactions are treated as nonbonded exceptions:
exception_pairs = []
for index in range(nonbonded.getNumExceptions()):
i, j, _, _, _ = nonbonded.getExceptionParameters(index)
if set([i, j]).issubset(solute_atoms):
exception_pairs.append(set([i, j]))
for i, j in itertools.combinations(solute_atoms, 2):
if set([i, j]) not in exception_pairs:
q1, sig1, eps1 = nonbonded.getParticleParameters(i)
q2, sig2, eps2 = nonbonded.getParticleParameters(j)
nonbonded.addException(i, j, q1 * q2, (sig1 + sig2) / 2,
np.sqrt(eps1 * eps2))
if use_softcore:
softcore.addExclusion(
i, j) # Needed for matching exception number
# Turn off or scale solute Lennard-Jones interactions, scale solute charges:
lj_parameters = dict()
charges = dict()
for index in solute_atoms:
charge, sigma, epsilon = nonbonded.getParticleParameters(index)
nonbonded.setParticleParameters(index, 0.0, 0.0, 0.0)
if charge / charge.unit != 0.0:
charges[index] = charge
if epsilon / epsilon.unit != 0.0:
lj_parameters[index] = (sigma, epsilon)
if charges:
nonbonded.addGlobalParameter('lambda_coul', 1.0)
for index, charge in charges.items():
nonbonded.addParticleParameterOffset('lambda_coul', index,
charge, 0.0, 0.0)
if lj_parameters and not use_softcore:
nonbonded.addGlobalParameter('lambda_vdw', 1.0)
for index, (sigma, epsilon) in lj_parameters.items():
nonbonded.addParticleParameterOffset('lambda_vdw', index, 0.0,
sigma, epsilon)
rcut = 10 * unit.angstroms
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)
from __future__ import print_function
import pytest
from simtk import openmm
from simtk import unit
from simtk.openmm import app
import atomsmm
def test_exceptions():
case = 'tests/data/emim_BCN4_Jiung2014'
pdb = app.PDBFile(case + '.pdb')
forcefield = app.ForceField(case + '.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=app.CutoffPeriodic)
force = atomsmm.forces.NonbondedExceptionsForce()
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(-27616.298459208883)
