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Commit 504d9c71 authored by Sunhwan Jo's avatar Sunhwan Jo
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add NBFIX/VSTIE2 handling

parent 76d0252c
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Showing with 212 additions and 9 deletions
wrappers/python/simtk/openmm/app/gromacstopfile.py
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...@@ -43,7 +43,8 @@ import math ...@@ -43,7 +43,8 @@ import math
import os import os
import re import re
import distutils.spawn import distutils.spawn
from collections import OrderedDict from collections import OrderedDict, defaultdict
from itertools import combinations
HBonds = ff.HBonds HBonds = ff.HBonds
AllBonds = ff.AllBonds AllBonds = ff.AllBonds
...@@ -115,7 +116,9 @@ class GromacsTopFile(object): ...@@ -115,7 +116,9 @@ class GromacsTopFile(object):
self.exclusions = [] self.exclusions = []
self.pairs = [] self.pairs = []
self.cmaps = [] self.cmaps = []
self.vsites2 = []
self.has_virtual_sites = False self.has_virtual_sites = False
self.has_nbfix_terms = False
def _processFile(self, file): def _processFile(self, file):
append = '' append = ''
...@@ -249,6 +252,10 @@ class GromacsTopFile(object): ...@@ -249,6 +252,10 @@ class GromacsTopFile(object):
self._processPairType(line) self._processPairType(line)
elif self._currentCategory == 'cmaptypes': elif self._currentCategory == 'cmaptypes':
self._processCmapType(line) self._processCmapType(line)
elif self._currentCategory == 'nonbond_params':
self._processNonbondType(line)
elif self._currentCategory == 'virtual_sites2':
self._processVirtualSites2(line)
elif self._currentCategory.startswith('virtual_sites'): elif self._currentCategory.startswith('virtual_sites'):
if self._currentMoleculeType is None: if self._currentMoleculeType is None:
raise ValueError('Found %s before [ moleculetype ]' % raise ValueError('Found %s before [ moleculetype ]' %
...@@ -435,6 +442,22 @@ class GromacsTopFile(object): ...@@ -435,6 +442,22 @@ class GromacsTopFile(object):
raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line) raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line)
self._cmapTypes[tuple(fields[:5])] = fields self._cmapTypes[tuple(fields[:5])] = fields
def _processNonbondType(self, line):
"""Process a line in the [ nonbond_params ] category."""
fields = line.split()
if len(fields) < 5:
raise ValueError('Too few fields in [ nonbond_params ] line: '+line)
if fields[2] != '1':
raise ValueError('Unsupported function type in [ nonbond_params ] line: '+line)
self._nonbondTypes[tuple(sorted(fields[:2]))] = fields
def _processVirtualSites2(self, line):
"""Process a line in the [ virtual_sites2 ] category."""
fields = line.split()
if len(fields) < 5:
raise ValueError('Too few fields in [ virtual_sites2 ] line: ' + line)
self._currentMoleculeType.vsites2.append(fields[:5])
def __init__(self, file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None): def __init__(self, file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None):
"""Load a top file. """Load a top file.
...@@ -484,6 +507,7 @@ class GromacsTopFile(object): ...@@ -484,6 +507,7 @@ class GromacsTopFile(object):
self._implicitTypes = {} self._implicitTypes = {}
self._pairTypes = {} self._pairTypes = {}
self._cmapTypes = {} self._cmapTypes = {}
self._nonbondTypes = {}
self._processFile(file) self._processFile(file)
# Create the Topology from it. # Create the Topology from it.
...@@ -643,6 +667,25 @@ class GromacsTopFile(object): ...@@ -643,6 +667,25 @@ class GromacsTopFile(object):
for types in dihedralTypeTable.values(): for types in dihedralTypeTable.values():
types.append(key) types.append(key)
# NBFIX
atom_types = []
for moleculeName, moleculeCount in self._molecules:
moleculeType = self._moleculeTypes[moleculeName]
for _ in range(moleculeCount):
for atom in moleculeType.atoms:
atom_types.append(atom[1])
has_nbfix_terms = any([pair in self._nonbondTypes for pair in combinations(sorted(atom_types), 2)])
has_nbfix_terms = True
if has_nbfix_terms:
# Build a lookup table and angle/dihedral indices list to
# let us handle exclusion manually.
angleIndices = []
torsionIndices = []
atom_partners = defaultdict(lambda : defaultdict(set))
atom_charges = []
# Loop over molecules and create the specified number of each type. # Loop over molecules and create the specified number of each type.
for moleculeName, moleculeCount in self._molecules: for moleculeName, moleculeCount in self._molecules:
...@@ -840,18 +883,25 @@ class GromacsTopFile(object): ...@@ -840,18 +883,25 @@ class GromacsTopFile(object):
for fields in moleculeType.atoms: for fields in moleculeType.atoms:
params = self._atomTypes[fields[1]] params = self._atomTypes[fields[1]]
if len(fields) > 6: if len(fields) > 6:
q = float(fields[6]) q = float(fields[6])
else: else:
q = float(params[4]) q = float(params[4])
if self._defaults[1] == '1': if has_nbfix_terms:
if self._defaults[1] != '2':
raise NotImplemented
nb.addParticle(q, 1.0, 0.0) nb.addParticle(q, 1.0, 0.0)
lj.addParticle([float(params[6]), float(params[7])]) atom_charges.append(q)
elif self._defaults[1] == '2': else:
nb.addParticle(q, float(params[6]), float(params[7])) 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]))
for fields in moleculeType.atoms:
if implicitSolvent is OBC2: if implicitSolvent is OBC2:
if fields[1] not in self._implicitTypes: if fields[1] not in self._implicitTypes:
raise ValueError('No implicit solvent parameters specified for atom type: '+fields[1]) raise ValueError('No implicit solvent parameters specified for atom type: '+fields[1])
...@@ -860,6 +910,23 @@ class GromacsTopFile(object): ...@@ -860,6 +910,23 @@ class GromacsTopFile(object):
for fields in moleculeType.bonds: for fields in moleculeType.bonds:
atoms = [int(x)-1 for x in fields[:2]] atoms = [int(x)-1 for x in fields[:2]]
bondIndices.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1])) bondIndices.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1]))
if has_nbfix_terms:
for fields in moleculeType.bonds:
atoms = [int(x)-1 for x in fields[:2]]
atom_partners[baseAtomIndex+atoms[0]]['bond'].add(baseAtomIndex+atoms[1])
atom_partners[baseAtomIndex+atoms[1]]['bond'].add(baseAtomIndex+atoms[0])
for fields in moleculeType.angles:
atoms = [int(x)-1 for x in fields[:3]]
angleIndices.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2]))
for pair in combinations(atoms, 2):
atom_partners[baseAtomIndex+pair[0]]['angle'].add(baseAtomIndex+pair[1])
atom_partners[baseAtomIndex+pair[1]]['angle'].add(baseAtomIndex+pair[0])
for fields in moleculeType.dihedrals:
atoms = [int(x)-1 for x in fields[:4]]
torsionIndices.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3]))
for pair in combinations(atoms, 2):
atom_partners[baseAtomIndex+pair[0]]['torsion'].add(baseAtomIndex+pair[1])
atom_partners[baseAtomIndex+pair[1]]['torsion'].add(baseAtomIndex+pair[0])
# Record nonbonded exceptions. # Record nonbonded exceptions.
...@@ -886,16 +953,70 @@ class GromacsTopFile(object): ...@@ -886,16 +953,70 @@ class GromacsTopFile(object):
if atom > atoms[0]: if atom > atoms[0]:
exclusions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom)) exclusions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom))
# Record virtual sites
for fields in moleculeType.vsites2:
atoms = [int(x)-1 for x in fields[:3]]
c1 = float(fields[4])
vsite = mm.TwoParticleAverageSite(baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], (1-c1), c1)
sys.setVirtualSite(baseAtomIndex+atoms[0], vsite)
# Create nonbonded exceptions. # Create nonbonded exceptions.
nb.createExceptionsFromBonds(bondIndices, fudgeQQ, fudgeLJ) if not has_nbfix_terms:
nb.createExceptionsFromBonds(bondIndices, fudgeQQ, fudgeLJ)
else:
excluded_atom_pairs = set() # save these pairs so we don't zero them out
for tor in torsionIndices:
# First check to see if atoms 1 and 4 are already excluded because
# they are 1-2 or 1-3 pairs (would happen in 6-member rings or
# fewer). Then check that they're not already added as exclusions
if 'bond' in atom_partners[tor[3]] and tor[0] in atom_partners[tor[3]]['bond']: continue
if 'angle' in atom_partners[tor[3]] and tor[0] in atom_partners[tor[3]]['angle']: continue
key = min((tor[0], tor[3]),
(tor[3], tor[0]))
if key in excluded_atom_pairs: continue # multiterm...
params1 = self._atomTypes[atom_types[tor[0]]]
params4 = self._atomTypes[atom_types[tor[3]]]
q1 = atom_charges[tor[0]]
rmin1 = float(params1[6])
eps1 = float(params1[7])
q4 = atom_charges[tor[3]]
rmin4 = float(params4[6])
eps4 = float(params4[7])
charge_prod = (q1*q4)
epsilon = (math.sqrt(abs(eps1 * eps4)))
rmin14 = (rmin1 + rmin4) / 2
nb.addException(tor[0], tor[3], charge_prod, rmin14, epsilon)
excluded_atom_pairs.add(key)
# Add excluded atoms
for atom_idx, atom in atom_partners.items():
# Exclude all bonds and angles
for atom2 in atom['bond']:
if atom2 > atom_idx:
nb.addException(atom_idx, atom2, 0.0, 1.0, 0.0)
excluded_atom_pairs.add((atom_idx, atom2))
for atom2 in atom['angle']:
if ((atom_idx, atom2) in excluded_atom_pairs):
continue
if atom2 > atom_idx:
nb.addException(atom_idx, atom2, 0.0, 1.0, 0.0)
excluded_atom_pairs.add((atom_idx, atom2))
for atom2 in atom['dihedral']:
if atom2 <= atom_idx: continue
if ((atom_idx, atom2) in excluded_atom_pairs):
continue
nb.addException(atom_idx, atom2, 0.0, 1.0, 0.0)
for exclusion in exclusions: for exclusion in exclusions:
nb.addException(exclusion[0], exclusion[1], 0.0, 1.0, 0.0, True) nb.addException(exclusion[0], exclusion[1], 0.0, 1.0, 0.0, True)
if self._defaults[1] == '1': if self._defaults[1] == '1':
# We're using a CustomNonbondedForce for LJ interactions, so also create a CustomBondForce # We're using a CustomNonbondedForce for LJ interactions, so also create a CustomBondForce
# to handle the exceptions. # to handle the exceptions.
pair_bond = mm.CustomBondForce('138.935456*q/r-C/r^6+A/r^12') pair_bond = mm.CustomBondForce('138.935456*q/r-C/r^6+A/r^12')
pair_bond.addPerBondParameter('q') pair_bond.addPerBondParameter('q')
pair_bond.addPerBondParameter('C') pair_bond.addPerBondParameter('C')
...@@ -932,6 +1053,88 @@ class GromacsTopFile(object): ...@@ -932,6 +1053,88 @@ class GromacsTopFile(object):
lj.setNonbondedMethod(methodMap[nonbondedMethod]) lj.setNonbondedMethod(methodMap[nonbondedMethod])
lj.setCutoffDistance(nonbondedCutoff) lj.setCutoffDistance(nonbondedCutoff)
if has_nbfix_terms:
if self._defaults[1] != '2':
raise NotImplemented
atom_nbfix_types = set([])
for pair in self._nonbondTypes:
atom_nbfix_types.add(pair[0])
atom_nbfix_types.add(pair[1])
lj_idx_list = [0 for _ in atom_types]
lj_radii, lj_depths = [], []
num_lj_types = 0
lj_type_list = []
for i,atom_type in enumerate(atom_types):
atom = self._atomTypes[atom_type]
if lj_idx_list[i]: continue # already assigned
atom_rmin = atom[6]
atom_epsilon = atom[7]
num_lj_types += 1
lj_idx_list[i] = num_lj_types
ljtype = (atom_rmin, atom_epsilon)
lj_type_list.append(atom)
lj_radii.append(float(atom_rmin))
lj_depths.append(float(atom_epsilon))
for j in range(i+1, len(atom_types)):
atom_type2 = atom_types[j]
if lj_idx_list[j] > 0: continue # already assigned
atom2 = self._atomTypes[atom_type2]
atom2_rmin = atom2[6]
atom2_epsilon = atom2[7]
if atom2 is atom:
lj_idx_list[j] = num_lj_types
elif atom_type not in atom_nbfix_types:
# Only non-NBFIXed atom types can be compressed
ljtype2 = (atom2_rmin, atom2_epsilon)
if ljtype == ljtype2:
lj_idx_list[j] = num_lj_types
# Now everything is assigned. Create the A-coefficient and
# B-coefficient arrays
acoef = [0 for i in range(num_lj_types*num_lj_types)]
bcoef = acoef[:]
for i in range(num_lj_types):
namei = lj_type_list[i][0]
for j in range(num_lj_types):
namej = lj_type_list[j][0]
try:
params = self._nonbondTypes[tuple(sorted((namei, namej)))]
rij = float(params[3])
wdij = float(params[4])
except KeyError:
rij = (lj_radii[i] + lj_radii[j]) / 2
wdij = math.sqrt(lj_depths[i] * lj_depths[j])
acoef[i+num_lj_types*j] = 2 * math.sqrt(wdij) * rij**6
bcoef[i+num_lj_types*j] = 4 * wdij * rij**6
cforce = mm.CustomNonbondedForce('(a/r6)^2-b/r6; r6=r^6;'
'a=acoef(type1, type2);'
'b=bcoef(type1, type2)')
cforce.addTabulatedFunction('acoef',
mm.Discrete2DFunction(num_lj_types, num_lj_types, acoef))
cforce.addTabulatedFunction('bcoef',
mm.Discrete2DFunction(num_lj_types, num_lj_types, bcoef))
cforce.addPerParticleParameter('type')
if (nonbondedMethod in (ff.PME, ff.LJPME, ff.Ewald, ff.CutoffPeriodic)):
cforce.setNonbondedMethod(cforce.CutoffPeriodic)
cforce.setCutoffDistance(nonbondedCutoff)
cforce.setUseLongRangeCorrection(True)
elif nonbondedMethod is ff.NoCutoff:
cforce.setNonbondedMethod(cforce.NoCutoff)
elif nonbondedMethod is ff.CutoffNonPeriodic:
cforce.setNonbondedMethod(cforce.CutoffNonPeriodic)
cforce.setCutoffDistance(nonbondedCutoff)
else:
raise ValueError('Unrecognized nonbonded method')
for i in lj_idx_list:
cforce.addParticle((i - 1,)) # adjust for indexing from 0
for i in range(nb.getNumExceptions()):
ii, jj, q, eps, sig = nb.getExceptionParameters(i)
cforce.addExclusion(ii, jj)
sys.addForce(cforce)
# Adjust masses. # Adjust masses.
if hydrogenMass is not None: if hydrogenMass is not None:
......
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