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Commit fbf193fe authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1778 from GrossfieldLab/improved-gromacs 

Improved gromacs
parents 792a9c07 4dcdf1d6
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Showing with 5278 additions and 20 deletions
wrappers/python/simtk/openmm/app/gromacsgrofile.py
View file @ fbf193fe
......@@ -69,11 +69,14 @@ def _is_gro_coord(line):
@param[in] line The line to be tested
"""
sline = line.split()
if len(sline) == 6 or len(sline) == 9:
return all([_isint(sline[2]), _isfloat(sline[3]), _isfloat(sline[4]), _isfloat(sline[5])])
elif len(sline) == 5 or len(sline) == 8:
return all([_isint(line[15:20]), _isfloat(sline[2]), _isfloat(sline[3]), _isfloat(sline[4])])
# data lines are fixed field
fields = []
fields.append(line[16:20].strip()) # atom number
fields.append(line[21:28].strip()) # x coord
fields.append(line[29:36].strip()) # y coord
fields.append(line[37:44].strip()) # z coord
if (all([f != '' for f in fields])): # check for empty fields
return all([_isint(fields[0]), _isfloat(fields[1]), _isfloat(fields[2]), _isfloat(fields[3])])
else:
return 0
......
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ fbf193fe
......@@ -258,11 +258,16 @@ class GromacsTopFile(object):
def _processDefaults(self, line):
"""Process the [ defaults ] line."""
fields = line.split()
if len(fields) < 4:
if len(fields) < 5:
# fudgeLJ and fudgeQQ not specified, assumed 1.0 by default
if len(fields) == 3:
fields.append(1.0)
fields.append(1.0)
else:
raise ValueError('Too few fields in [ defaults ] line: '+line)
if fields[0] != '1':
raise ValueError('Unsupported nonbonded type: '+fields[0])
if fields[1] != '2':
if not (fields[1] == '2' or fields[1] == '1'):
raise ValueError('Unsupported combination rule: '+fields[1])
if fields[2].lower() == 'no':
self._genpairs = False
......@@ -570,7 +575,7 @@ class GromacsTopFile(object):
The solvent dielectric constant to use in the implicit solvent
model.
ewaldErrorTolerance : float=0.0005
The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
The error tolerance to use if nonbondedMethod is Ewald, PME or LJPME.
removeCMMotion : boolean=True
If true, a CMMotionRemover will be added to the System
hydrogenMass : mass=None
......@@ -593,6 +598,11 @@ class GromacsTopFile(object):
raise ValueError('Illegal nonbonded method for a non-periodic system')
nb = mm.NonbondedForce()
sys.addForce(nb)
if self._defaults[1] == '1':
lj = mm.CustomNonbondedForce('sqrt(A1*A2)/r^12-sqrt(C1*C2)/r^6')
lj.addPerParticleParameter('C')
lj.addPerParticleParameter('A')
sys.addForce(lj)
if implicitSolvent is OBC2:
gb = mm.GBSAOBCForce()
gb.setSoluteDielectric(soluteDielectric)
......@@ -610,8 +620,10 @@ class GromacsTopFile(object):
mapIndices = {}
bondIndices = []
topologyAtoms = list(self.topology.atoms())
exceptions = []
exclusions = []
pairs = []
fudgeQQ = float(self._defaults[4])
fudgeLJ = float(self._defaults[3])
# Build a lookup table to let us process dihedrals more quickly.
......@@ -748,7 +760,7 @@ class GromacsTopFile(object):
dihedralType = fields[4]
reversedTypes = types[::-1]+(dihedralType,)
types = types+(dihedralType,)
if (dihedralType in ('1', '2', '4', '9') and len(fields) > 7) or (dihedralType == '3' and len(fields) > 10):
if (dihedralType in ('1', '4', '9') and len(fields) > 7) or (dihedralType == '3' and len(fields) > 10) or (dihedralType == '2' and len(fields) > 6):
paramsList = [fields]
else:
# Look for a matching dihedral type.
......@@ -776,13 +788,16 @@ class GromacsTopFile(object):
elif dihedralType == '2':
# Harmonic torsion
k = float(params[6])
phi0 = float(params[5])
if k != 0:
if harmonicTorsion is None:
harmonicTorsion = mm.CustomTorsionForce('0.5*k*(theta-theta0)^2')
harmonicTorsion = mm.CustomTorsionForce('0.5*k*(thetap-theta0)^2; thetap = step(-(theta-theta0+pi))*2*pi+theta+step(theta-theta0-pi)*(-2*pi); pi = %.15g' % math.pi)
harmonicTorsion.addPerTorsionParameter('theta0')
harmonicTorsion.addPerTorsionParameter('k')
sys.addForce(harmonicTorsion)
harmonicTorsion.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], (float(params[5])*degToRad, k))
# map phi0 into correct space
phi0 = phi0 - 360 if phi0 > 180 else phi0
harmonicTorsion.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], (phi0*degToRad, k))
else:
# RB Torsion
c = [float(x) for x in params[5:11]]
......@@ -825,11 +840,18 @@ class GromacsTopFile(object):
for fields in moleculeType.atoms:
params = self._atomTypes[fields[1]]
if len(fields) > 6:
q = float(fields[6])
else:
q = float(params[4])
if self._defaults[1] == '1':
nb.addParticle(q, 1.0, 0.0)
lj.addParticle([float(params[6]), float(params[7])])
elif self._defaults[1] == '2':
nb.addParticle(q, float(params[6]), float(params[7]))
if implicitSolvent is OBC2:
if fields[1] not in self._implicitTypes:
raise ValueError('No implicit solvent parameters specified for atom type: '+fields[1])
......@@ -857,19 +879,37 @@ class GromacsTopFile(object):
continue # We'll use the automatically generated parameters
atom1params = nb.getParticleParameters(baseAtomIndex+atoms[0])
atom2params = nb.getParticleParameters(baseAtomIndex+atoms[1])
exceptions.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], atom1params[0]*atom2params[0]*fudgeQQ, params[0], params[1]))
pairs.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], atom1params[0]*atom2params[0]*fudgeQQ, params[0], params[1]))
for fields in moleculeType.exclusions:
atoms = [int(x)-1 for x in fields]
for atom in atoms[1:]:
if atom > atoms[0]:
exceptions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom, 0, 0, 0))
exclusions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom))
# Create nonbonded exceptions.
nb.createExceptionsFromBonds(bondIndices, fudgeQQ, float(self._defaults[3]))
for exception in exceptions:
nb.addException(exception[0], exception[1], exception[2], float(exception[3]), float(exception[4]), True)
nb.createExceptionsFromBonds(bondIndices, fudgeQQ, fudgeLJ)
for exclusion in exclusions:
nb.addException(exclusion[0], exclusion[1], 0.0, 1.0, 0.0, True)
if self._defaults[1] == '1':
# We're using a CustomNonbondedForce for LJ interactions, so also create a CustomBondForce
# to handle the exceptions.
pair_bond = mm.CustomBondForce('138.935456*q/r-C/r^6+A/r^12')
pair_bond.addPerBondParameter('q')
pair_bond.addPerBondParameter('C')
pair_bond.addPerBondParameter('A')
sys.addForce(pair_bond)
lj.createExclusionsFromBonds(bondIndices, 3)
for pair in pairs:
nb.addException(pair[0], pair[1], pair[2], 1.0, 0.0, True)
pair_bond.addBond(pair[0], pair[1], [pair[2],float(pair[3]), float(pair[4])])
for exclusion in exclusions:
lj.addExclusion(exclusion[0], exclusion[1])
elif self._defaults[1] == '2':
for pair in pairs:
nb.addException(pair[0], pair[1], pair[2], float(pair[3]), float(pair[4]), True)
# Finish configuring the NonbondedForce.
......@@ -882,6 +922,15 @@ class GromacsTopFile(object):
nb.setNonbondedMethod(methodMap[nonbondedMethod])
nb.setCutoffDistance(nonbondedCutoff)
nb.setEwaldErrorTolerance(ewaldErrorTolerance)
if self._defaults[1] == '1':
methodMap = {ff.NoCutoff:mm.CustomNonbondedForce.NoCutoff,
ff.CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic,
ff.CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic,
ff.Ewald:mm.CustomNonbondedForce.CutoffPeriodic,
ff.PME:mm.CustomNonbondedForce.CutoffPeriodic,
ff.LJPME:mm.CustomNonbondedForce.CutoffPeriodic}
lj.setNonbondedMethod(methodMap[nonbondedMethod])
lj.setCutoffDistance(nonbondedCutoff)
# Adjust masses.
......
wrappers/python/tests/TestGromacsTopFile.py
View file @ fbf193fe
......@@ -51,6 +51,18 @@ class TestGromacsTopFile(unittest.TestCase):
ene = context.getState(getEnergy=True, groups=2**1).getPotentialEnergy()
self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 341.6905133582857)
def test_SMOG(self):
""" Test to ensure that SMOG models can be run without problems """
top = GromacsTopFile('systems/2ci2.pdb.top')
gro = GromacsGroFile('systems/2ci2.pdb.gro')
system = top.createSystem()
context = Context(system, VerletIntegrator(1*femtosecond),
Platform.getPlatformByName('Reference'))
context.setPositions(gro.positions)
ene = context.getState(getEnergy=True).getPotentialEnergy()
self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), -346.940915296)
def test_Cutoff(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
......
wrappers/python/tests/systems/2ci2.pdb.gro 0 → 100644
View file @ fbf193fe
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wrappers/python/tests/systems/2ci2.pdb.top 0 → 100644
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