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 test_SolvationSystem():
system, positions, topology, solute = readSystem(
'hydroxyethylaminoanthraquinone-in-water')
solvation_system = atomsmm.SolvationSystem(system, solute)
state = dict(lambda_vdw=0.5, lambda_coul=0.5)
components = atomsmm.splitPotentialEnergy(solvation_system, topology,
positions, **state)
potential = dict()
potential['HarmonicBondForce'] = 1815.1848188179738
potential['HarmonicAngleForce'] = 1111.5544374007236
potential['PeriodicTorsionForce'] = 1.5998609986459567
potential['Real-Space'] = 58273.35327317236
potential['Reciprocal-Space'] = -76436.3982762784
potential['CustomNonbondedForce'] = -64.67189605331785
potential['Total'] = -15299.377781942014
for term, value in components.items():
assert value / value.unit == pytest.approx(potential[term])
def test_SolvationSystem_with_lj_parameter_scaling():
system, positions, topology, solute = readSystem(
'hydroxyethylaminoanthraquinone-in-water')
solvation_system = atomsmm.SolvationSystem(system,
solute,
use_softcore=False)
state = dict(lambda_vdw=0.5, lambda_coul=0.5)
components = atomsmm.splitPotentialEnergy(solvation_system, topology,
positions, **state)
potential = dict()
potential['HarmonicBondForce'] = 1815.1848188179738
potential['HarmonicAngleForce'] = 1111.5544374007236
potential['PeriodicTorsionForce'] = 1.5998609986459567
potential['Real-Space'] = 58235.03496195241
potential['Reciprocal-Space'] = -76436.3982762784
potential['Total'] = -15273.024197108643
for term, value in components.items():
assert value / value.unit == pytest.approx(potential[term])
def test_RESPASystem():
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)
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'] = 58161.10011792888
potential['Reciprocal-Space'] = -76436.3982762784
potential['CustomNonbondedForce'] = -64.67189605331785
potential['CustomNonbondedForce(1)'] = -17294.836032921234
potential['CustomNonbondedForce(2)'] = 17294.836032921194
potential['CustomBondForce'] = 112.25315524350334
potential['Total'] = -15299.377781942032
for term, value in components.items():
assert value / value.unit == pytest.approx(potential[term])
def test_RESPASystem_with_lj_parameter_scaling():
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,
use_softcore=False)
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'] = 58122.78180670893
potential['Reciprocal-Space'] = -76436.3982762784
potential['CustomNonbondedForce'] = -17317.054135213173
potential['CustomNonbondedForce(1)'] = 17317.054135213126
potential['CustomBondForce'] = 112.25315524350334
potential['Total'] = -15273.024197108669
for term, value in components.items():
assert value / value.unit == pytest.approx(potential[term])
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]
else:
respa_system = solvation_system
for force in respa_system.getForces():
if isinstance(force, openmm.NonbondedForce):
force.setReciprocalSpaceForceGroup(1)
force.setForceGroup(1)
loops = [2 * args.timestep, 1]
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=True,
softcore_group=1,
split_exceptions=True)
if args.timestep <= 3:
respa_system = solvation_system
for force in solvation_system.getForces():
if isinstance(force, openmm.NonbondedForce):
force.setReciprocalSpaceForceGroup(1)
force.setForceGroup(1)
loops = [2 * args.timestep, 1]
else:
respa_system = atomsmm.RESPASystem(solvation_system,
rcutIn,
rswitchIn,
fastExceptions=True)
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=True,
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)
if barostatInterval > 0:
barostat = openmm.MonteCarloBarostat(1*unit.atmospheres, temp, barostatInterval)
solvation_system.addForce(barostat)
integrator = openmm.LangevinIntegrator(temp, 1.0/unit.picoseconds, dt)
simulation = openmm.app.Simulation(pdb.topology, solvation_system, integrator, platform, properties)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(temp)
states_data = pd.read_csv(f'{base}.states', sep='\s+', comment='#')
parameterStates = states_data[['lambda_vdw', 'lambda_coul']]
simulate = states_data['simulate']
for state in reversed(states_data.index):