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 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 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_AlchemicalRespaSystem_without_middle_scale():
system, positions, topology, solute = readSystem('phenol-in-water')
respa_info = dict(rcutIn=7 * unit.angstroms, rswitchIn=5 * unit.angstroms)
solvation_system = atomsmm.systems.AlchemicalRespaSystem(
system,
*respa_info.values(),
solute,
coupling_function='lambda^4*(5-4*lambda)',
middle_scale=False,
)
state = {'lambda': 0.5}
components = atomsmm.splitPotentialEnergy(solvation_system, topology,
positions, **state)
for item in components.items():
print(*item)
potential = {}
potential['HarmonicBondForce'] = 2621.3223922886677 # kJ/mol
potential['HarmonicAngleForce'] = 1525.1006876561419 # kJ/mol
potential['PeriodicTorsionForce'] = 18.767576693568476 # kJ/mol
potential['Real-Space'] = 80089.51116719692 # kJ/mol
potential['Reciprocal-Space'] = -107038.52551657759 # kJ/mol
potential['CustomBondForce'] = -53.526446723139806 # kJ/mol
potential['CustomCVForce'] = -7.114065227572182 # kJ/mol
potential['Total'] = -22844.464204692995 # kJ/mol
for term, value in components.items():
assert value / value.unit == pytest.approx(potential[term])
def test_AlchemicalRespaSystem():
system, positions, topology, solute = readSystem('phenol-in-water')
respa_info = dict(rcutIn=7 * unit.angstroms, rswitchIn=5 * unit.angstroms)
solvation_system = atomsmm.systems.AlchemicalRespaSystem(
system,
*respa_info.values(),
solute,
coupling_function='lambda^4*(5-4*lambda)',
)
state = {'lambda': 0.5, 'respa_switch': 1}
components = atomsmm.splitPotentialEnergy(solvation_system, topology,
positions, **state)
for item in components.items():
print(*item)
potential = {}
potential['HarmonicBondForce'] = 2621.3223922886677 # kJ/mol
potential['HarmonicAngleForce'] = 1525.1006876561419 # kJ/mol
potential['PeriodicTorsionForce'] = 18.767576693568476 # kJ/mol
potential['Real-Space'] = 80089.51116719692 # kJ/mol
potential['Reciprocal-Space'] = -107038.52551657759 # kJ/mol
potential['CustomNonbondedForce'] = 5037.152491649265 # kJ/mol
potential['CustomBondForce'] = -53.526446723139806 # kJ/mol
potential['CustomBondForce(1)'] = -53.374675325650806 # kJ/mol
potential['CustomCVForce'] = -7.114065227572182 # kJ/mol
potential['CustomCVForce(1)'] = -6.301336948673654 # kJ/mol
potential['Total'] = -17866.987725318053 # kJ/mol
for term, value in components.items():
assert value / value.unit == pytest.approx(potential[term])
def test_RESPASystem_with_special_bonds():
system, positions, topology, solute = readSystem('q-SPC-FW')
respa_info = dict(rcutIn=7 * unit.angstroms, rswitchIn=5 * unit.angstroms)
respa_system = atomsmm.RESPASystem(system, *respa_info.values())
respa_system.redefine_bond(topology, 'HOH', 'H[1-2]', 'O',
1.05 * unit.angstroms)
respa_system.redefine_angle(topology, 'HOH', 'H[1-2]', 'O', 'H[1-2]',
113 * unit.degrees)
components = atomsmm.splitPotentialEnergy(respa_system, topology,
positions)
potential = dict()
potential['HarmonicBondForce'] = 3665.684696323676
potential['HarmonicAngleForce'] = 1811.197218501007
potential['PeriodicTorsionForce'] = 0.0
potential['Real-Space'] = 84694.39953220935
potential['Reciprocal-Space'] = -111582.71281220087
potential['CustomNonbondedForce'] = -25531.129587235544
potential['CustomNonbondedForce(1)'] = 25531.129587235544
potential['CustomBondForce'] = 0.0
potential['CustomBondForce(1)'] = -1175.253817235862
potential['CustomAngleForce'] = -305.0221912655623
potential['Total'] = -22891.707373668243
for term, value in components.items():
print(term, value)
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_AlchemicalRespaSystem_with_softcore():
system, positions, topology, solute = readSystem('phenol-in-water')
respa_info = dict(rcutIn=7 * unit.angstroms, rswitchIn=5 * unit.angstroms)
solvation_system = atomsmm.systems.AlchemicalRespaSystem(
system,
*respa_info.values(),
solute,
use_softcore=True,
)
state = {'lambda': 0.5, 'respa_switch': 1}
components = atomsmm.splitPotentialEnergy(solvation_system, topology,
positions, **state)
platform = openmm.Platform.getPlatformByName('Reference')
context = openmm.Context(system, openmm.CustomIntegrator(0), platform)
context.setPositions(positions)
force = solvation_system.get_alchemical_vdw_force(
[i / 5 for i in range(6)])
values = force.getCollectiveVariableValues(
context) * unit.kilojoules_per_mole
for index in range(force.getNumCollectiveVariables()):
name = force.getCollectiveVariableName(index)
components[name] = values[index]
for item in components.items():
print(*item)
potential = {}
potential['HarmonicBondForce'] = 2621.3223922886677 # kJ/mol
potential['HarmonicAngleForce'] = 1525.1006876561419 # kJ/mol
potential['PeriodicTorsionForce'] = 18.767576693568476 # kJ/mol
potential['Real-Space'] = 80089.51116719692 # kJ/mol
potential['Reciprocal-Space'] = -107038.52551657759 # kJ/mol
potential['CustomNonbondedForce'] = 5037.152491649265 # kJ/mol
potential['CustomBondForce'] = -53.526446723139806 # kJ/mol
potential['CustomBondForce(1)'] = -53.374675325650806 # kJ/mol
potential['CustomNonbondedForce(1)'] = -24.140118811594814 # kJ/mol
potential['CustomNonbondedForce(2)'] = -24.140118811594814 # kJ/mol
potential['Total'] = -17901.852560765 # kJ/mol
potential['E0'] = 0.0 # kJ/mol
potential['E1'] = -10.071581499620784 # kJ/mol
potential['E2'] = -19.66450283710424 # kJ/mol
potential['E3'] = -28.284595753200428 # kJ/mol
potential['E4'] = -35.004158250494505 # kJ/mol
potential['E5'] = -37.9416812137183 # kJ/mol
for term, value in components.items():
assert value / value.unit == pytest.approx(potential[term])
def test_AlchemicalRespaSystem_with_coulomb_scaling():
system, positions, topology, solute = readSystem('phenol-in-water')
respa_info = dict(rcutIn=7 * unit.angstroms, rswitchIn=5 * unit.angstroms)
solvation_system = atomsmm.systems.AlchemicalRespaSystem(
system,
*respa_info.values(),
solute,
coupling_function='lambda^4*(5-4*lambda)',
coulomb_scaling=True,
lambda_coul=0.5,
# middle_scale=True,
)
state = {'lambda': 0.5, 'respa_switch': 1}
components = atomsmm.splitPotentialEnergy(solvation_system, topology,
positions, **state)
integrator = openmm.CustomIntegrator(0)
platform = openmm.Platform.getPlatformByName('Reference')
simulation = openmm.app.Simulation(topology, solvation_system, integrator,
platform)
simulation.context.setPositions(positions)
force = solvation_system.get_alchemical_coul_force()
Ecoul = force.getCollectiveVariableValues(simulation.context)
components['Ecoul'] = Ecoul[0] * unit.kilojoule_per_mole
for item in components.items():
print(*item)
potential = {}
potential['HarmonicBondForce'] = 2621.3223922886677 # kJ/mol
potential['HarmonicAngleForce'] = 1525.1006876561419 # kJ/mol
potential['PeriodicTorsionForce'] = 18.767576693568476 # kJ/mol
potential['Real-Space'] = 80078.91697014398 # kJ/mol
potential['Reciprocal-Space'] = -107074.49398119976 # kJ/mol
potential['CustomNonbondedForce'] = 5037.152491649265 # kJ/mol
potential['CustomBondForce'] = -53.526446723139806 # kJ/mol
potential['CustomBondForce(1)'] = -53.374675325650806 # kJ/mol
potential['CustomNonbondedForce(1)'] = -23.447733015522058 # kJ/mol
potential['CustomCVForce'] = -7.114065227572182 # kJ/mol
potential['CustomCVForce(1)'] = -6.301336948673654 # kJ/mol
potential['Total'] = -17936.998120008684 # kJ/mol
potential['Ecoul'] = -93.14060537915793 # kJ/mol
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])
def _minimizeOverlaps(self, platform, membrane):
hydrogen_mass = 3 * unit.amu
system = self.structure.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=1 *
unit.nanometer,
rigidWater=True,
flexibleConstraints=False,
constraints=app.HBonds,
hydrogenMass=hydrogen_mass,
removeCMMotion=False)
backup_system = deepcopy(system)
for index in self.atom_to_freeze:
system.setParticleMass(int(index), 0.0 * unit.dalton)
integrator = mm.LangevinIntegrator(300 * unit.kelvin,
1.0 / unit.picoseconds,
2 * unit.femtosecond)
simulation = app.Simulation(self.structure.topology, system,
integrator, platform)
simulation.context.setPositions(self.structure.positions)
simulation.minimizeEnergy(tolerance=0.1 * unit.kilojoule / unit.mole,
maxIterations=0)
positions = simulation.context.getState(
getPositions=True).getPositions()
min_potential = atomsmm.splitPotentialEnergy(system,
self.structure.topology,
positions)
for key, value in min_potential.items():
self.logger.debug(key, value)
simulation.saveCheckpoint('porinMembraneSystem.chk')
integrator = mm.LangevinIntegrator(300 * unit.kelvin,
1.0 / unit.picoseconds,
2 * unit.femtosecond)
simulation = app.Simulation(self.structure.topology, backup_system,
integrator, platform)
simulation.context.setPositions(positions)
simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)
simulation.reporters.append(
app.StateDataReporter(
'relax-ligand-system.log',
100,
step=True,
temperature=True,
potentialEnergy=True,
totalEnergy=True,
speed=True,
))
topology = md.Topology.from_openmm(self.structure.topology)
atom_indices = topology.select('(protein and not resname ' +
membrane + ')' + ' or resname ' +
self.lig_name)
simulation.reporters.append(
NetCDFReporter('relax-ligand-system.nc',
100,
atomSubset=atom_indices))
simulation.step(100000)
positions = simulation.context.getState(
getPositions=True).getPositions()
PDBxFile.writeFile(self.structure.topology, positions,
open("atomistic-system-combined.pdbx", 'w'))
simulation = app.Simulation(modeller.topology, system, integrator, platform)
simulation.context.setPositions(modeller.positions)
simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)
# Minimize the system after adding hydrogens to the membrane
tolerance = 0.1 * unit.kilojoules_per_mole / unit.angstroms
simulation.minimizeEnergy(tolerance=tolerance, maxIterations=0)
simulation.reporters.append(
app.StateDataReporter('relax-hydrogens.log',
1000,
step=True,
temperature=True,
potentialEnergy=True,
totalEnergy=True,
speed=True))
simulation.step(10000)
positions = simulation.context.getState(getPositions=True).getPositions()
min_potential = atomsmm.splitPotentialEnergy(system, modeller.topology,
positions)
for key, value in min_potential.items():
logger.debug(key, value)
logger.debug(modeller.topology)
simulation.saveCheckpoint('state.chk')
#del simulation.context, integrator
# rigidWater = False is necessary because water parameters are required by Parmed
# when loading the ligand
#system = forcefield.createSystem(modeller.topology,
# nonbondedMethod=app.PME,
# rigidWater=False,
# nonbondedCutoff=1*unit.nanometer)
#ligand_atomistic_system = PorinMembraneSystem('comp7', system, modeller.topology, positions, platform, membrane = 'DPPC')