Skip to content

GitLab

Commit 9e6762f9 authored by Zheng Gong's avatar Zheng Gong
Browse files

Construct 1-3 and 1-4 exclusion pairs from bond instead of angle and dihedral

parent 83b8ea75
Hide whitespace changes
Inline Side-by-side
Showing with 72 additions and 59 deletions
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 9e6762f9
......@@ -164,6 +164,7 @@ class CharmmPsfFile(object):
CMAP_FORCE_GROUP = 5
NONBONDED_FORCE_GROUP = 6
GB_FORCE_GROUP = 6
DRUDE_FORCE_GROUP = 7
@_catchindexerror
def __init__(self, psf_name, periodicBoxVectors=None, unitCellDimensions=None):
......@@ -466,6 +467,37 @@ class CharmmPsfFile(object):
else:
self.box_vectors = periodicBoxVectors
def _build_exclusion_list(self):
pair_12_set = set()
pair_13_set = set()
pair_14_set = set()
for bond in self.bond_list:
a1, a2 = bond.atom1, bond.atom2
pair = (min(a1.idx, a2.idx), max(a1.idx, a2.idx),)
pair_12_set.add(pair)
for bond in self.bond_list:
a2, a3 = bond.atom1, bond.atom2
for a1 in a2.bond_partners:
pair = (min(a1.idx, a3.idx), max(a1.idx, a3.idx),)
if a1 != a3:
pair_13_set.add(pair)
for a4 in a3.bond_partners:
pair = (min(a2.idx, a4.idx), max(a2.idx, a4.idx),)
if a2 != a4:
pair_13_set.add(pair)
for bond in self.bond_list:
a2, a3 = bond.atom1, bond.atom2
for a1 in a2.bond_partners:
for a4 in a3.bond_partners:
pair = (min(a1.idx, a4.idx), max(a1.idx, a4.idx),)
if a1 != a4:
pair_14_set.add(pair)
# in case there are 3,4,5-member rings
self.pair_12_list = list(sorted(pair_12_set))
self.pair_13_list = list(sorted(pair_13_set - pair_12_set))
self.pair_14_list = list(sorted(pair_14_set - pair_13_set.union(pair_12_set)))
@staticmethod
def _convert(string, type, message):
"""Converts a string to a specific type, making sure to raise
......@@ -1320,31 +1352,29 @@ class CharmmPsfFile(object):
# now, add the actual force to the system
system.addForce(nbtforce)
# build 1-2, 1-3 and 1-4 pairs from connectivity
if verbose:
print('Build exclusion list...')
self._build_exclusion_list()
if verbose:
print('\tNumber of 1-2 pairs: %i' % len(self.pair_12_list))
print('\tNumber of 1-3 pairs: %i' % len(self.pair_13_list))
print('\tNumber of 1-4 pairs: %i' % len(self.pair_14_list))
# Add 1-4 interactions
excluded_atom_pairs = set() # save these pairs so we don't zero them out
sigma_scale = 2**(-1/6)
nbxmod = abs(params.nbxmod)
if nbxmod == 4:
for ia1, ia4 in self.pair_14_list:
force.addException(ia1, ia4, 0.0, 0.1, 0.0)
if nbxmod == 5:
for tor in self.dihedral_parameter_list:
# 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 tor.atom1 in tor.atom4.bond_partners: continue
if tor.atom1 in tor.atom4.angle_partners: continue
key = min((tor.atom1.idx, tor.atom4.idx),
(tor.atom4.idx, tor.atom1.idx))
if key in excluded_atom_pairs: continue # multiterm...
charge_prod = (tor.atom1.charge * tor.atom4.charge)
epsilon = (sqrt(abs(tor.atom1.type.epsilon_14) * ene_conv *
abs(tor.atom4.type.epsilon_14) * ene_conv))
sigma = (tor.atom1.type.rmin_14 + tor.atom4.type.rmin_14) * (
length_conv * sigma_scale)
force.addException(tor.atom1.idx, tor.atom4.idx,
charge_prod, sigma, epsilon)
excluded_atom_pairs.add(
min((tor.atom1.idx, tor.atom4.idx),
(tor.atom4.idx, tor.atom1.idx))
)
for ia1, ia4 in self.pair_14_list:
atom1 = self.atom_list[ia1]
atom4 = self.atom_list[ia4]
charge_prod = (atom1.charge * atom4.charge)
epsilon = sqrt(abs(atom1.type.epsilon_14 * atom4.type.epsilon_14)) * ene_conv
sigma = (atom1.type.rmin_14 + atom4.type.rmin_14) * (length_conv * sigma_scale)
force.addException(ia1, ia4, charge_prod, sigma, epsilon)
# Add excluded atoms
# Drude and lonepairs will be excluded based on their parent atoms
......@@ -1368,33 +1398,24 @@ class CharmmPsfFile(object):
for i in range(len(excludeterm)):
for j in range(i):
force.addException(excludeterm[j], excludeterm[i], 0.0, 0.1, 0.0)
# Exclude all bonds and angles, as well as the lonepair/Drude attached onto them
for atom in self.atom_list:
if nbxmod > 1:
for atom2 in atom.bond_partners:
if atom2.idx > atom.idx:
for excludeatom in [atom.idx]+parent_exclude_list[atom.idx]:
for excludeatom2 in [atom2.idx]+parent_exclude_list[atom2.idx]:
force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0)
if nbxmod > 2:
for atom2 in atom.angle_partners:
if atom2.idx > atom.idx:
for excludeatom in [atom.idx]+parent_exclude_list[atom.idx]:
for excludeatom2 in [atom2.idx]+parent_exclude_list[atom2.idx]:
force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0)
if nbxmod > 3:
for atom2 in atom.dihedral_partners:
if atom2.idx <= atom.idx: continue
if ((atom.idx, atom2.idx) in excluded_atom_pairs):
continue
force.addException(atom.idx, atom2.idx, 0.0, 0.1, 0.0)
# Exclude 1-2 and 1-3 pairs as well as the lonepair/Drude attached onto them
if nbxmod > 1:
for ia1, ia2 in self.pair_12_list:
for excludeatom in [ia1]+parent_exclude_list[ia1]:
for excludeatom2 in [ia2]+parent_exclude_list[ia2]:
force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0)
if nbxmod > 2:
for ia1, ia3 in self.pair_13_list:
for excludeatom in [ia1]+parent_exclude_list[ia1]:
for excludeatom2 in [ia3]+parent_exclude_list[ia3]:
force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0)
system.addForce(force)
# Add Drude particles (Drude force)
if has_drude_particle:
if verbose: print('Adding Drude force and Thole screening...')
drudeforce = mm.DrudeForce()
drudeforce.setForceGroup(7)
drudeforce.setForceGroup(self.DRUDE_FORCE_GROUP)
for pair in self.drudepair_list:
parentatom=pair[0]
drudeatom=pair[1]
......@@ -1423,24 +1444,16 @@ class CharmmPsfFile(object):
particleMap = {}
for i in range(drudeforce.getNumParticles()):
particleMap[drudeforce.getParticleParameters(i)[0]] = i
for bond in self.bond_list:
alpha1 = self.drudeconsts_list[bond.atom1.idx][0]
alpha2 = self.drudeconsts_list[bond.atom2.idx][0]
if abs(alpha1) > TINY and abs(alpha2) > TINY: # both are Drude parent atoms
thole1 = self.drudeconsts_list[bond.atom1.idx][1]
thole2 = self.drudeconsts_list[bond.atom2.idx][1]
drude1 = bond.atom1.idx + 1 # CHARMM psf has hard-coded rule that the Drude is next to its parent
drude2 = bond.atom2.idx + 1
drudeforce.addScreenedPair(particleMap[drude1], particleMap[drude2], thole1+thole2)
for ang in self.angle_list:
alpha1 = self.drudeconsts_list[ang.atom1.idx][0]
alpha2 = self.drudeconsts_list[ang.atom3.idx][0]
# Apply thole screening for 1-2 and 1-3 pairs
for ia1, ia2 in self.pair_12_list + self.pair_13_list:
alpha1 = self.drudeconsts_list[ia1][0]
alpha2 = self.drudeconsts_list[ia2][0]
if abs(alpha1) > TINY and abs(alpha2) > TINY: # both are Drude parent atoms
thole1 = self.drudeconsts_list[ang.atom1.idx][1]
thole2 = self.drudeconsts_list[ang.atom3.idx][1]
drude1 = ang.atom1.idx + 1 # CHARMM psf has hard-coded rule that the Drude is next to its parent
drude2 = ang.atom3.idx + 1
thole1 = self.drudeconsts_list[ia1][1]
thole2 = self.drudeconsts_list[ia2][1]
drude1 = ia1 + 1 # CHARMM psf has hard-coded rule that the Drude is next to its parent
drude2 = ia2 + 1
drudeforce.addScreenedPair(particleMap[drude1], particleMap[drude2], thole1+thole2)
# If we needed a CustomNonbondedForce, map all of the exceptions from
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment