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"openmmapi/src/CustomManyParticleForceImpl.cpp" did not exist on "99cebd08f8949f4984fe862601046e89620678d2"
Unverified Commit fde2ca6d authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2615 from YevChern/master 

Fix for CharmmPsfFile parser constrains with CHARMM TIP3 water topology
parents 7bf58d51 53de9f14
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wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ fde2ca6d
......@@ -272,6 +272,9 @@ class CharmmPsfFile(object):
drudepair_list.append([min(id1,id2), max(id1,id2)])
elif (atom_list[id1].name[0:2]=='LP' or atom_list[id2].name[0:2]=='LP' or atom_list[id1].name=='OM' or atom_list[id2].name=='OM'):
pass
# Ignore H-H bond in water if present
elif atom_list[id1].name[0]=='H' and atom_list[id2].name[0]=='H' and (atom_list[id1].residue.resname in WATNAMES):
pass
else:
bond_list.append(Bond(atom_list[id1], atom_list[id2]))
bond_list.changed = False
......
wrappers/python/tests/TestCharmmFiles.py
View file @ fde2ca6d
......@@ -422,6 +422,114 @@ class TestCharmmFiles(unittest.TestCase):
self.assertEqual(sorted(system.getConstraintParameters(i)[:2] for i in range(system.getNumConstraints())),
sorted(hBonds_water + hAngles_water + allBonds_methanol + hAngles_methanol))
def test_Constraints_charmm(self):
"""Tests that CHARMM and OpenMM implementation of CHARMM force field produce the same constraints and energy"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ala3_solv.psf',
unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500) * angstroms)
crd = CharmmCrdFile('systems/ala3_solv.crd')
params = CharmmParameterSet('systems/par_all36_prot.prm',
'systems/toppar_water_ions.str')
plat = Platform.getPlatformByName('Reference')
system_charmm = psf.createSystem(params, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
topology = psf.topology
forcefield = ForceField('charmm36.xml', 'charmm36/water.xml')
system_openmm = forcefield.createSystem(topology, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
# Test different combinations of constrains/rigidWater parameters
system_charmm = psf.createSystem(params, constraints=None, rigidWater=False, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
system_openmm = forcefield.createSystem(topology, constraints=None, rigidWater=False, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
self.assertEqual(system_charmm.getNumConstraints(), 0)
self.assertEqual(system_openmm.getNumConstraints(), 0)
con_charmm = Context(system_charmm, VerletIntegrator(2 * femtoseconds), plat)
con_charmm.setPositions(crd.positions)
con_openmm = Context(system_openmm, VerletIntegrator(2 * femtoseconds), plat)
con_openmm.setPositions(crd.positions)
state_charmm = con_charmm.getState(getEnergy=True, enforcePeriodicBox=True)
ene_charmm = state_charmm.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
state_openmm = con_openmm.getState(getEnergy=True, enforcePeriodicBox=True)
ene_openmm = state_openmm.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene_charmm, ene_openmm, delta=0.05)
system_charmm = psf.createSystem(params, constraints=None, rigidWater=True, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
system_openmm = forcefield.createSystem(topology, constraints=None, rigidWater=True, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
self.assertEqual(
sorted(system_charmm.getConstraintParameters(i)[:2] for i in range(system_charmm.getNumConstraints())),
sorted(system_openmm.getConstraintParameters(j)[:2] for j in range(system_openmm.getNumConstraints())))
for i in range(system_charmm.getNumConstraints()):
self.assertAlmostEqual(system_charmm.getConstraintParameters(i)[2],
system_openmm.getConstraintParameters(i)[2], delta=1e-7 * nanometers)
system_charmm = psf.createSystem(params, constraints=HBonds, rigidWater=False, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
system_openmm = forcefield.createSystem(topology, constraints=HBonds, rigidWater=False, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
self.assertEqual(
sorted(system_charmm.getConstraintParameters(i)[:2] for i in range(system_charmm.getNumConstraints())),
sorted(system_openmm.getConstraintParameters(j)[:2] for j in range(system_openmm.getNumConstraints())))
for i in range(system_charmm.getNumConstraints()):
self.assertAlmostEqual(system_charmm.getConstraintParameters(i)[2],
system_openmm.getConstraintParameters(i)[2], delta=1e-7 * nanometers)
system_charmm = psf.createSystem(params, constraints=HBonds, rigidWater=True, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
system_openmm = forcefield.createSystem(topology, constraints=HBonds, rigidWater=True, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
self.assertEqual(
sorted(system_charmm.getConstraintParameters(i)[:2] for i in range(system_charmm.getNumConstraints())),
sorted(system_openmm.getConstraintParameters(j)[:2] for j in range(system_openmm.getNumConstraints())))
for i in range(system_charmm.getNumConstraints()):
self.assertAlmostEqual(system_charmm.getConstraintParameters(i)[2],
system_openmm.getConstraintParameters(i)[2], delta=1e-7 * nanometers)
system_charmm = psf.createSystem(params, constraints=AllBonds, rigidWater=False, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
system_openmm = forcefield.createSystem(topology, constraints=AllBonds, rigidWater=False, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
self.assertEqual(
sorted(system_charmm.getConstraintParameters(i)[:2] for i in range(system_charmm.getNumConstraints())),
sorted(system_openmm.getConstraintParameters(j)[:2] for j in range(system_openmm.getNumConstraints())))
for i in range(system_charmm.getNumConstraints()):
self.assertAlmostEqual(system_charmm.getConstraintParameters(i)[2],
system_openmm.getConstraintParameters(i)[2], delta=1e-7 * nanometers)
system_charmm = psf.createSystem(params, constraints=AllBonds, rigidWater=True, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
system_openmm = forcefield.createSystem(topology, constraints=AllBonds, rigidWater=True, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
self.assertEqual(
sorted(system_charmm.getConstraintParameters(i)[:2] for i in range(system_charmm.getNumConstraints())),
sorted(system_openmm.getConstraintParameters(j)[:2] for j in range(system_openmm.getNumConstraints())))
for i in range(system_charmm.getNumConstraints()):
self.assertAlmostEqual(system_charmm.getConstraintParameters(i)[2],
system_openmm.getConstraintParameters(i)[2], delta=1e-7 * nanometers)
system_charmm = psf.createSystem(params, constraints=HAngles, rigidWater=False, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
system_openmm = forcefield.createSystem(topology, constraints=HAngles, rigidWater=False, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
self.assertEqual(
sorted(system_charmm.getConstraintParameters(i)[:2] for i in range(system_charmm.getNumConstraints())),
sorted(system_openmm.getConstraintParameters(j)[:2] for j in range(system_openmm.getNumConstraints())))
for i in range(system_charmm.getNumConstraints()):
self.assertAlmostEqual(system_charmm.getConstraintParameters(i)[2],
system_openmm.getConstraintParameters(i)[2], delta=1e-7 * nanometers)
system_charmm = psf.createSystem(params, constraints=HAngles, rigidWater=True, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
system_openmm = forcefield.createSystem(topology, constraints=HAngles, rigidWater=True, nonbondedMethod=PME,
nonbondedCutoff=8 * angstroms)
self.assertEqual(
sorted(system_charmm.getConstraintParameters(i)[:2] for i in range(system_charmm.getNumConstraints())),
sorted(system_openmm.getConstraintParameters(j)[:2] for j in range(system_openmm.getNumConstraints())))
for i in range(system_charmm.getNumConstraints()):
self.assertAlmostEqual(system_charmm.getConstraintParameters(i)[2],
system_openmm.getConstraintParameters(i)[2], delta=1e-7 * nanometers)
if __name__ == '__main__':
unittest.main()
......
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