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Unverified Commit 8dd60914 authored by Tristan Croll's avatar Tristan Croll Committed by GitHub
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Merge pull request #3 from openmm/master 

Sync with official repo
parents 3475b790 75c1fcb6
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Showing with 976 additions and 189 deletions
tests/TestVariableLangevinIntegrator.h
View file @ 8dd60914
...@@ -310,6 +310,24 @@ void testArgonBox() { ...@@ -310,6 +310,24 @@ void testArgonBox() {
ke /= 1000; ke /= 1000;
double expected = 1.5 * numParticles * BOLTZ * temp; double expected = 1.5 * numParticles * BOLTZ * temp;
ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.01); ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.01);
// Compute the mean step size.
double meanStep = 0;
for (int i = 0; i < 100; i++) {
integrator.step(1);
meanStep += integrator.getStepSize();
}
meanStep /= 100;
double maxStep = meanStep/2;
// Now set a limit on the step size and see if it is obeyed.
integrator.setMaximumStepSize(maxStep);
for (int i = 0; i < 100; i++) {
integrator.step(1);
ASSERT(integrator.getStepSize() <= maxStep*1.000001);
}
} }
void runPlatformTests(); void runPlatformTests();
......
tests/TestVariableVerletIntegrator.h
View file @ 8dd60914
...@@ -289,6 +289,24 @@ void testArgonBox() { ...@@ -289,6 +289,24 @@ void testArgonBox() {
double energy = state.getKineticEnergy() + state.getPotentialEnergy(); double energy = state.getKineticEnergy() + state.getPotentialEnergy();
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
} }
// Compute the mean step size.
double meanStep = 0;
for (int i = 0; i < 100; i++) {
integrator.step(1);
meanStep += integrator.getStepSize();
}
meanStep /= 100;
double maxStep = meanStep/2;
// Now set a limit on the step size and see if it is obeyed.
integrator.setMaximumStepSize(maxStep);
for (int i = 0; i < 100; i++) {
integrator.step(1);
ASSERT(integrator.getStepSize() <= maxStep*1.000001);
}
} }
void runPlatformTests(); void runPlatformTests();
......
wrappers/Doxyfile.in
View file @ 8dd60914
...@@ -582,7 +582,7 @@ INPUT_ENCODING = UTF-8 ...@@ -582,7 +582,7 @@ INPUT_ENCODING = UTF-8
# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
FILE_PATTERNS = FILE_PATTERNS = *.h
# The RECURSIVE tag can be used to turn specify whether or not subdirectories # The RECURSIVE tag can be used to turn specify whether or not subdirectories
# should be searched for input files as well. Possible values are YES and NO. # should be searched for input files as well. Possible values are YES and NO.
......
wrappers/python/simtk/openmm/app/__init__.py
View file @ 8dd60914
...@@ -6,7 +6,7 @@ from __future__ import absolute_import ...@@ -6,7 +6,7 @@ from __future__ import absolute_import
__docformat__ = "epytext en" __docformat__ = "epytext en"
__author__ = "Peter Eastman" __author__ = "Peter Eastman"
__copyright__ = "Copyright 2016, Stanford University and Peter Eastman" __copyright__ = "Copyright 2016-2019, Stanford University and Peter Eastman"
__credits__ = [] __credits__ = []
__license__ = "MIT" __license__ = "MIT"
__maintainer__ = "Peter Eastman" __maintainer__ = "Peter Eastman"
...@@ -32,6 +32,8 @@ from .checkpointreporter import CheckpointReporter ...@@ -32,6 +32,8 @@ from .checkpointreporter import CheckpointReporter
from .charmmcrdfiles import CharmmCrdFile, CharmmRstFile from .charmmcrdfiles import CharmmCrdFile, CharmmRstFile
from .charmmparameterset import CharmmParameterSet from .charmmparameterset import CharmmParameterSet
from .charmmpsffile import CharmmPsfFile, CharmmPSFWarning from .charmmpsffile import CharmmPsfFile, CharmmPSFWarning
from .simulatedtempering import SimulatedTempering
from .metadynamics import Metadynamics, BiasVariable
# Enumerated values # Enumerated values
......
wrappers/python/simtk/openmm/app/charmmcrdfiles.py
View file @ 8dd60914
...@@ -47,7 +47,7 @@ ONE_TIMESCALE = 1 / TIMESCALE ...@@ -47,7 +47,7 @@ ONE_TIMESCALE = 1 / TIMESCALE
class CharmmCrdFile(object): class CharmmCrdFile(object):
""" """
Reads and parses a CHARMM coordinate file (.crd) into its components, Reads and parses a CHARMM coordinate file (.crd) into its components,
namely the coordinates, CHARMM atom types, resid, resname, etc. namely the coordinates, CHARMM atom types, resname, etc.
Attributes Attributes
---------- ----------
...@@ -69,7 +69,6 @@ class CharmmCrdFile(object): ...@@ -69,7 +69,6 @@ class CharmmCrdFile(object):
self.atomno = [] # Atom number self.atomno = [] # Atom number
self.resno = [] # Residue number self.resno = [] # Residue number
self.resname = [] # Residue name self.resname = [] # Residue name
self.resid = [] # Residue ID
self.attype = [] # Atom type self.attype = [] # Atom type
self.positions = [] # 3N atomic coordinates self.positions = [] # 3N atomic coordinates
self.title = [] # .crd file title block self.title = [] # .crd file title block
...@@ -105,7 +104,7 @@ class CharmmCrdFile(object): ...@@ -105,7 +104,7 @@ class CharmmCrdFile(object):
try: try:
self.natom = int(line.strip().split()[0]) self.natom = int(line.strip().split()[0])
for row in range(self.natom): for _ in range(self.natom):
line = crdfile.readline().strip().split() line = crdfile.readline().strip().split()
self.atomno.append(int(line[0])) self.atomno.append(int(line[0]))
self.resno.append(int(line[1])) self.resno.append(int(line[1]))
...@@ -114,7 +113,6 @@ class CharmmCrdFile(object): ...@@ -114,7 +113,6 @@ class CharmmCrdFile(object):
pos = Vec3(float(line[4]), float(line[5]), float(line[6])) pos = Vec3(float(line[4]), float(line[5]), float(line[6]))
self.positions.append(pos) self.positions.append(pos)
self.segid.append(line[7]) self.segid.append(line[7])
self.resid.append(int(line[8]))
self.weighting.append(float(line[9])) self.weighting.append(float(line[9]))
if self.natom != len(self.positions): if self.natom != len(self.positions):
...@@ -124,7 +122,7 @@ class CharmmCrdFile(object): ...@@ -124,7 +122,7 @@ class CharmmCrdFile(object):
len(self.positions)) len(self.positions))
) )
except (ValueError, IndexError) as e: except (ValueError, IndexError):
raise CharmmFileError('Error parsing CHARMM coordinate file') raise CharmmFileError('Error parsing CHARMM coordinate file')
# Apply units to the positions now. Do it this way to allow for # Apply units to the positions now. Do it this way to allow for
......
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ 8dd60914
...@@ -116,6 +116,7 @@ class CharmmParameterSet(object): ...@@ -116,6 +116,7 @@ class CharmmParameterSet(object):
self.nbfix_types = dict() self.nbfix_types = dict()
self.nbthole_types = dict() self.nbthole_types = dict()
self.parametersets = [] self.parametersets = []
self.nbxmod = 5
# Load all of the files # Load all of the files
tops, pars, strs = [], [], [] tops, pars, strs = [], [], []
...@@ -228,8 +229,17 @@ class CharmmParameterSet(object): ...@@ -228,8 +229,17 @@ class CharmmParameterSet(object):
nonbonded_types = dict() # Holder nonbonded_types = dict() # Holder
parameterset = None parameterset = None
read_first_nonbonded = False read_first_nonbonded = False
previous = ''
for line in f: for line in f:
line = line.strip() line = previous+line.strip()
previous = ''
if line.endswith('-'):
# This will be continued on the next line.
previous = line[:-1]
continue
if line.startswith('!'):
# This is a comment.
continue
if not line: if not line:
# This is a blank line # This is a blank line
continue continue
...@@ -258,6 +268,12 @@ class CharmmParameterSet(object): ...@@ -258,6 +268,12 @@ class CharmmParameterSet(object):
if line.startswith('NONBONDED'): if line.startswith('NONBONDED'):
read_first_nonbonded = False read_first_nonbonded = False
section = 'NONBONDED' section = 'NONBONDED'
fields = line.upper().split()
if 'NBXMOD' in fields:
nbxmod = int(fields[fields.index('NBXMOD')+1])
if nbxmod not in list(range(-5, 6)):
raise CharmmFileError('Unsupported value for NBXMOD: %d' % nbxmod)
self.nbxmod = nbxmod
continue continue
if line.startswith('NBFIX'): if line.startswith('NBFIX'):
section = 'NBFIX' section = 'NBFIX'
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 8dd60914
...@@ -166,7 +166,7 @@ class CharmmPsfFile(object): ...@@ -166,7 +166,7 @@ class CharmmPsfFile(object):
GB_FORCE_GROUP = 6 GB_FORCE_GROUP = 6
@_catchindexerror @_catchindexerror
def __init__(self, psf_name): def __init__(self, psf_name, periodicBoxVectors=None, unitCellDimensions=None):
"""Opens and parses a PSF file, then instantiates a CharmmPsfFile """Opens and parses a PSF file, then instantiates a CharmmPsfFile
instance from the data. instance from the data.
...@@ -174,6 +174,11 @@ class CharmmPsfFile(object): ...@@ -174,6 +174,11 @@ class CharmmPsfFile(object):
---------- ----------
psf_name : str psf_name : str
Name of the PSF file (it must exist) Name of the PSF file (it must exist)
periodicBoxVectors : tuple of Vec3
the vectors defining the periodic box
unitCellDimensions : Vec3
the dimensions of the crystallographic unit cell. For
non-rectangular unit cells, specify periodicBoxVectors instead.
Raises Raises
------ ------
...@@ -358,7 +363,10 @@ class CharmmPsfFile(object): ...@@ -358,7 +363,10 @@ class CharmmPsfFile(object):
set_molecules(atom_list) set_molecules(atom_list)
molecule_list = [atom.marked for atom in atom_list] molecule_list = [atom.marked for atom in atom_list]
if len(holder) == len(atom_list): if len(holder) == len(atom_list):
if molecule_list != holder: if len(molecule_list) != len(holder):
# The MOLNT section is only used for fluctuating charge models,
# which are currently not supported anyway.
# Therefore, we only check the lengths of the lists now rather than their contents.
warnings.warn('Detected PSF molecule section that is WRONG. ' warnings.warn('Detected PSF molecule section that is WRONG. '
'Resetting molecularity.', CharmmPSFWarning) 'Resetting molecularity.', CharmmPSFWarning)
# We have a CHARMM PSF file; now do NUMLP/NUMLPH sections # We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
...@@ -449,7 +457,14 @@ class CharmmPsfFile(object): ...@@ -449,7 +457,14 @@ class CharmmPsfFile(object):
self.group_list = group_list self.group_list = group_list
self.title = title self.title = title
self.flags = psf_flags self.flags = psf_flags
self.box_vectors = None if unitCellDimensions is not None:
if periodicBoxVectors is not None:
raise ValueError("specify either periodicBoxVectors or unitCellDimensions, but not both")
if u.is_quantity(unitCellDimensions):
unitCellDimensions = unitCellDimensions.value_in_unit(u.nanometers)
self.box_vectors = (Vec3(unitCellDimensions[0], 0, 0), Vec3(0, unitCellDimensions[1], 0), Vec3(0, 0, unitCellDimensions[2]))*u.nanometers
else:
self.box_vectors = periodicBoxVectors
@staticmethod @staticmethod
def _convert(string, type, message): def _convert(string, type, message):
...@@ -710,7 +725,7 @@ class CharmmPsfFile(object): ...@@ -710,7 +725,7 @@ class CharmmPsfFile(object):
last_residue = None last_residue = None
if resid != last_residue: if resid != last_residue:
last_residue = resid last_residue = resid
residue = topology.addResidue(atom.residue.resname, chain, resid) residue = topology.addResidue(atom.residue.resname, chain, str(atom.residue.idx), atom.residue.inscode)
if atom.type is not None: if atom.type is not None:
# This is the most reliable way of determining the element # This is the most reliable way of determining the element
atomic_num = atom.type.atomic_number atomic_num = atom.type.atomic_number
...@@ -919,7 +934,7 @@ class CharmmPsfFile(object): ...@@ -919,7 +934,7 @@ class CharmmPsfFile(object):
atom1=lpsite[1] atom1=lpsite[1]
atom2=lpsite[2] atom2=lpsite[2]
atom3=lpsite[3] atom3=lpsite[3]
if atom3 > 0: if atom3 >= 0:
if lpsite[4] > 0 : # relative lonepair type if lpsite[4] > 0 : # relative lonepair type
r = lpsite[4] /10.0 # in nanometer r = lpsite[4] /10.0 # in nanometer
xweights = [-1.0, 0.0, 1.0] xweights = [-1.0, 0.0, 1.0]
...@@ -1082,6 +1097,7 @@ class CharmmPsfFile(object): ...@@ -1082,6 +1097,7 @@ class CharmmPsfFile(object):
# Add nonbonded terms now # Add nonbonded terms now
if verbose: print('Adding nonbonded interactions...') if verbose: print('Adding nonbonded interactions...')
force = mm.NonbondedForce() force = mm.NonbondedForce()
force.setUseDispersionCorrection(False)
force.setForceGroup(self.NONBONDED_FORCE_GROUP) force.setForceGroup(self.NONBONDED_FORCE_GROUP)
if not hasbox: # non-periodic if not hasbox: # non-periodic
if nonbondedMethod is ff.NoCutoff: if nonbondedMethod is ff.NoCutoff:
...@@ -1221,7 +1237,6 @@ class CharmmPsfFile(object): ...@@ -1221,7 +1237,6 @@ class CharmmPsfFile(object):
if (nonbondedMethod in (ff.PME, ff.LJPME, ff.Ewald, ff.CutoffPeriodic)): if (nonbondedMethod in (ff.PME, ff.LJPME, ff.Ewald, ff.CutoffPeriodic)):
cforce.setNonbondedMethod(cforce.CutoffPeriodic) cforce.setNonbondedMethod(cforce.CutoffPeriodic)
cforce.setCutoffDistance(nonbondedCutoff) cforce.setCutoffDistance(nonbondedCutoff)
cforce.setUseLongRangeCorrection(True)
elif nonbondedMethod is ff.NoCutoff: elif nonbondedMethod is ff.NoCutoff:
cforce.setNonbondedMethod(cforce.NoCutoff) cforce.setNonbondedMethod(cforce.NoCutoff)
elif nonbondedMethod is ff.CutoffNonPeriodic: elif nonbondedMethod is ff.CutoffNonPeriodic:
...@@ -1308,26 +1323,28 @@ class CharmmPsfFile(object): ...@@ -1308,26 +1323,28 @@ class CharmmPsfFile(object):
# Add 1-4 interactions # Add 1-4 interactions
excluded_atom_pairs = set() # save these pairs so we don't zero them out excluded_atom_pairs = set() # save these pairs so we don't zero them out
sigma_scale = 2**(-1/6) sigma_scale = 2**(-1/6)
for tor in self.dihedral_parameter_list: nbxmod = abs(params.nbxmod)
# First check to see if atoms 1 and 4 are already excluded because if nbxmod == 5:
# they are 1-2 or 1-3 pairs (would happen in 6-member rings or for tor in self.dihedral_parameter_list:
# fewer). Then check that they're not already added as exclusions # First check to see if atoms 1 and 4 are already excluded because
if tor.atom1 in tor.atom4.bond_partners: continue # they are 1-2 or 1-3 pairs (would happen in 6-member rings or
if tor.atom1 in tor.atom4.angle_partners: continue # fewer). Then check that they're not already added as exclusions
key = min((tor.atom1.idx, tor.atom4.idx), if tor.atom1 in tor.atom4.bond_partners: continue
(tor.atom4.idx, tor.atom1.idx)) if tor.atom1 in tor.atom4.angle_partners: continue
if key in excluded_atom_pairs: continue # multiterm... key = min((tor.atom1.idx, tor.atom4.idx),
charge_prod = (tor.atom1.charge * tor.atom4.charge) (tor.atom4.idx, tor.atom1.idx))
epsilon = (sqrt(abs(tor.atom1.type.epsilon_14) * ene_conv * if key in excluded_atom_pairs: continue # multiterm...
abs(tor.atom4.type.epsilon_14) * ene_conv)) charge_prod = (tor.atom1.charge * tor.atom4.charge)
sigma = (tor.atom1.type.rmin_14 + tor.atom4.type.rmin_14) * ( epsilon = (sqrt(abs(tor.atom1.type.epsilon_14) * ene_conv *
length_conv * sigma_scale) abs(tor.atom4.type.epsilon_14) * ene_conv))
force.addException(tor.atom1.idx, tor.atom4.idx, sigma = (tor.atom1.type.rmin_14 + tor.atom4.type.rmin_14) * (
charge_prod, sigma, epsilon) length_conv * sigma_scale)
excluded_atom_pairs.add( force.addException(tor.atom1.idx, tor.atom4.idx,
min((tor.atom1.idx, tor.atom4.idx), charge_prod, sigma, epsilon)
(tor.atom4.idx, tor.atom1.idx)) excluded_atom_pairs.add(
) min((tor.atom1.idx, tor.atom4.idx),
(tor.atom4.idx, tor.atom1.idx))
)
# Add excluded atoms # Add excluded atoms
# Drude and lonepairs will be excluded based on their parent atoms # Drude and lonepairs will be excluded based on their parent atoms
...@@ -1353,21 +1370,24 @@ class CharmmPsfFile(object): ...@@ -1353,21 +1370,24 @@ class CharmmPsfFile(object):
force.addException(excludeterm[j], excludeterm[i], 0.0, 0.1, 0.0) 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 # Exclude all bonds and angles, as well as the lonepair/Drude attached onto them
for atom in self.atom_list: for atom in self.atom_list:
for atom2 in atom.bond_partners: if nbxmod > 1:
if atom2.idx > atom.idx: for atom2 in atom.bond_partners:
for excludeatom in [atom.idx]+parent_exclude_list[atom.idx]: if atom2.idx > atom.idx:
for excludeatom2 in [atom2.idx]+parent_exclude_list[atom2.idx]: for excludeatom in [atom.idx]+parent_exclude_list[atom.idx]:
force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0) for excludeatom2 in [atom2.idx]+parent_exclude_list[atom2.idx]:
for atom2 in atom.angle_partners: force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0)
if atom2.idx > atom.idx: if nbxmod > 2:
for excludeatom in [atom.idx]+parent_exclude_list[atom.idx]: for atom2 in atom.angle_partners:
for excludeatom2 in [atom2.idx]+parent_exclude_list[atom2.idx]: if atom2.idx > atom.idx:
force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0) for excludeatom in [atom.idx]+parent_exclude_list[atom.idx]:
for atom2 in atom.dihedral_partners: for excludeatom2 in [atom2.idx]+parent_exclude_list[atom2.idx]:
if atom2.idx <= atom.idx: continue force.addException(excludeatom, excludeatom2, 0.0, 0.1, 0.0)
if ((atom.idx, atom2.idx) in excluded_atom_pairs): if nbxmod > 3:
continue for atom2 in atom.dihedral_partners:
force.addException(atom.idx, atom2.idx, 0.0, 0.1, 0.0) 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)
system.addForce(force) system.addForce(force)
# Add Drude particles (Drude force) # Add Drude particles (Drude force)
......
wrappers/python/simtk/openmm/app/data/charmm36.xml
View file @ 8dd60914
...@@ -102920,7 +102920,7 @@ ...@@ -102920,7 +102920,7 @@
<Torsion map="6" type1="C" type2="NH1" type3="CT" type4="C" type5="NH1"/> <Torsion map="6" type1="C" type2="NH1" type3="CT" type4="C" type5="NH1"/>
<Torsion map="7" type1="C" type2="N" type3="CT2" type4="C" type5="N"/> <Torsion map="7" type1="C" type2="N" type3="CT2" type4="C" type5="N"/>
</CMAPTorsionForce> </CMAPTorsionForce>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0"> <NonbondedForce coulomb14scale="1.0" lj14scale="1.0" useDispersionCorrection="False">
<UseAttributeFromResidue name="charge"/> <UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.0" sigma="1.0" type="H"/> <Atom epsilon="0.0" sigma="1.0" type="H"/>
<Atom epsilon="0.0" sigma="1.0" type="HC"/> <Atom epsilon="0.0" sigma="1.0" type="HC"/>
...@@ -103335,7 +103335,7 @@ ...@@ -103335,7 +103335,7 @@
<Atom epsilon="0.0" sigma="1.0" type="NE"/> <Atom epsilon="0.0" sigma="1.0" type="NE"/>
<Atom epsilon="0.0" sigma="1.0" type="DUM"/> <Atom epsilon="0.0" sigma="1.0" type="DUM"/>
</NonbondedForce> </NonbondedForce>
<LennardJonesForce lj14scale="1.0"> <LennardJonesForce lj14scale="1.0" useDispersionCorrection="False">
<Atom epsilon="0.192464" sigma="0.04000135244450124" type="H"/> <Atom epsilon="0.192464" sigma="0.04000135244450124" type="H"/>
<Atom epsilon="0.192464" sigma="0.04000135244450124" type="HC"/> <Atom epsilon="0.192464" sigma="0.04000135244450124" type="HC"/>
<Atom epsilon="0.092048" sigma="0.2351972615890496" type="HA"/> <Atom epsilon="0.092048" sigma="0.2351972615890496" type="HA"/>
wrappers/python/simtk/openmm/app/data/charmm_polar_2013.xml
View file @ 8dd60914
...@@ -7200,7 +7200,7 @@ ...@@ -7200,7 +7200,7 @@
<Torsion map="2" class1="CD2O1A" class2="ND3A3" class3="CD31C" class4="CD2O1A" class5="ND2A2"/> <Torsion map="2" class1="CD2O1A" class2="ND3A3" class3="CD31C" class4="CD2O1A" class5="ND2A2"/>
<Torsion map="2" class1="CD2O1A" class2="ND3A3" class3="CD31C" class4="CD2O1A" class5="ND3A3"/> <Torsion map="2" class1="CD2O1A" class2="ND3A3" class3="CD31C" class4="CD2O1A" class5="ND3A3"/>
</CMAPTorsionForce> </CMAPTorsionForce>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0"> <NonbondedForce coulomb14scale="1.0" lj14scale="1.0" useDispersionCorrection="False">
<Atom type="0" charge="1.71639" sigma="1.0" epsilon="1.0"/> <Atom type="0" charge="1.71639" sigma="1.0" epsilon="1.0"/>
<Atom type="1" charge="-1.11466" sigma="1.0" epsilon="1.0"/> <Atom type="1" charge="-1.11466" sigma="1.0" epsilon="1.0"/>
<Atom type="2" charge="0.55733" sigma="1.0" epsilon="1.0"/> <Atom type="2" charge="0.55733" sigma="1.0" epsilon="1.0"/>
...@@ -11370,6 +11370,7 @@ sigma14 = [ ...@@ -11370,6 +11370,7 @@ sigma14 = [
   
customNonbondedForce = mm.CustomNonbondedForce('4*eps*((sig/r)^12-(sig/r)^6); eps=epsilon(type1, type2); sig=sigma(type1, type2)') customNonbondedForce = mm.CustomNonbondedForce('4*eps*((sig/r)^12-(sig/r)^6); eps=epsilon(type1, type2); sig=sigma(type1, type2)')
customNonbondedForce.setNonbondedMethod(min(nonbondedForce.getNonbondedMethod(), 2)) customNonbondedForce.setNonbondedMethod(min(nonbondedForce.getNonbondedMethod(), 2))
customNonbondedForce.setUseLongRangeCorrection(False)
customNonbondedForce.setCutoffDistance(nonbondedForce.getCutoffDistance()) customNonbondedForce.setCutoffDistance(nonbondedForce.getCutoffDistance())
customNonbondedForce.addTabulatedFunction('epsilon', mm.Discrete2DFunction(numAtomClasses, numAtomClasses, epsilon)) customNonbondedForce.addTabulatedFunction('epsilon', mm.Discrete2DFunction(numAtomClasses, numAtomClasses, epsilon))
customNonbondedForce.addTabulatedFunction('sigma', mm.Discrete2DFunction(numAtomClasses, numAtomClasses, sigma)) customNonbondedForce.addTabulatedFunction('sigma', mm.Discrete2DFunction(numAtomClasses, numAtomClasses, sigma))
wrappers/python/simtk/openmm/app/data/pdbNames.xml
View file @ 8dd60914
...@@ -239,19 +239,19 @@ ...@@ -239,19 +239,19 @@
<Atom name="HN2" alt1="2H" alt2="HT2" alt3="H2"/> <Atom name="HN2" alt1="2H" alt2="HT2" alt3="H2"/>
</Residue> </Residue>
<Residue name="UNK" type="Protein"/> <Residue name="UNK" type="Protein"/>
<Residue name="A" alt1="ADE" type="Nucleic"> <Residue name="A" alt1="ADE" alt2="A3" alt3="A5" type="Nucleic">
<Atom name="H61" alt1="1H6"/> <Atom name="H61" alt1="1H6"/>
<Atom name="H62" alt1="2H6"/> <Atom name="H62" alt1="2H6"/>
</Residue> </Residue>
<Residue name="G" alt1="GUA" type="Nucleic"> <Residue name="G" alt1="GUA" alt2="G3" alt3="G5" type="Nucleic">
<Atom name="H21" alt1="1H2"/> <Atom name="H21" alt1="1H2"/>
<Atom name="H22" alt1="2H2"/> <Atom name="H22" alt1="2H2"/>
</Residue> </Residue>
<Residue name="C" alt1="CYT" type="Nucleic"> <Residue name="C" alt1="CYT" alt2="C3" alt3="C5" type="Nucleic">
<Atom name="H41" alt1="1H4"/> <Atom name="H41" alt1="1H4"/>
<Atom name="H42" alt1="2H4"/> <Atom name="H42" alt1="2H4"/>
</Residue> </Residue>
<Residue name="U" alt1="URA" type="Nucleic"/> <Residue name="U" alt1="URA" alt2="U3" alt3="U5" type="Nucleic"/>
<Residue name="DA" alt1="DAD" alt2="DA3" alt3="DA5" type="Nucleic"> <Residue name="DA" alt1="DAD" alt2="DA3" alt3="DA5" type="Nucleic">
<Atom name="H61" alt1="1H6"/> <Atom name="H61" alt1="1H6"/>
<Atom name="H62" alt1="2H6"/> <Atom name="H62" alt1="2H6"/>
......
wrappers/python/simtk/openmm/app/dcdreporter.py
View file @ 8dd60914
...@@ -101,7 +101,10 @@ class DCDReporter(object): ...@@ -101,7 +101,10 @@ class DCDReporter(object):
""" """
if self._dcd is None: if self._dcd is None:
self._dcd = DCDFile(self._out, simulation.topology, simulation.integrator.getStepSize(), 0, self._reportInterval, self._append) self._dcd = DCDFile(
self._out, simulation.topology, simulation.integrator.getStepSize(),
simulation.currentStep, self._reportInterval, self._append
)
self._dcd.writeModel(state.getPositions(), periodicBoxVectors=state.getPeriodicBoxVectors()) self._dcd.writeModel(state.getPositions(), periodicBoxVectors=state.getPeriodicBoxVectors())
def __del__(self): def __del__(self):
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 8dd60914
...@@ -37,6 +37,7 @@ import os ...@@ -37,6 +37,7 @@ import os
import itertools import itertools
import xml.etree.ElementTree as etree import xml.etree.ElementTree as etree
import math import math
import warnings
from math import sqrt, cos from math import sqrt, cos
from copy import deepcopy from copy import deepcopy
from collections import defaultdict from collections import defaultdict
...@@ -634,6 +635,29 @@ class ForceField(object): ...@@ -634,6 +635,29 @@ class ForceField(object):
atom = self.getAtomIndexByName(atom_name) atom = self.getAtomIndexByName(atom_name)
self.addExternalBond(atom) self.addExternalBond(atom)
def areParametersIdentical(self, template2, matchingAtoms, matchingAtoms2):
"""Get whether this template and another one both assign identical atom types and parameters to all atoms.
Parameters
----------
template2: _TemplateData
the template to compare this one to
matchingAtoms: list
the indices of atoms in this template that atoms of the residue are matched to
matchingAtoms2: list
the indices of atoms in template2 that atoms of the residue are matched to
"""
atoms1 = [self.atoms[m] for m in matchingAtoms]
atoms2 = [template2.atoms[m] for m in matchingAtoms2]
if any(a1.type != a2.type or a1.parameters != a2.parameters for a1,a2 in zip(atoms1, atoms2)):
return False
# Properly comparing virtual sites really needs a much more complicated analysis. This simple check
# could easily fail for templates containing vsites, even if they're actually identical. Since we
# currently have no force fields that include both patches and vsites, I'm not going to worry about it now.
if self.virtualSites != template2.virtualSites:
return False
return True
class _TemplateAtomData(object): class _TemplateAtomData(object):
"""Inner class used to encapsulate data about an atom in a residue template definition.""" """Inner class used to encapsulate data about an atom in a residue template definition."""
def __init__(self, name, type, element, parameters={}): def __init__(self, name, type, element, parameters={}):
...@@ -868,7 +892,7 @@ class ForceField(object): ...@@ -868,7 +892,7 @@ class ForceField(object):
Returns Returns
------- -------
template : _ForceFieldTemplate template : _TemplateData
The matching forcefield residue template, or None if no matches are found. The matching forcefield residue template, or None if no matches are found.
matches : list matches : list
a list specifying which atom of the template each atom of the residue a list specifying which atom of the template each atom of the residue
...@@ -890,7 +914,13 @@ class ForceField(object): ...@@ -890,7 +914,13 @@ class ForceField(object):
template = allMatches[0][0] template = allMatches[0][0]
matches = allMatches[0][1] matches = allMatches[0][1]
elif len(allMatches) > 1: elif len(allMatches) > 1:
raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) # We found multiple matches. This is OK if and only if they assign identical types and parameters to all atoms.
t1, m1 = allMatches[0]
for t2, m2 in allMatches[1:]:
if not t1.areParametersIdentical(t2, m1, m2):
raise Exception('Multiple non-identical matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))
template = allMatches[0][0]
matches = allMatches[0][1]
return [template, matches] return [template, matches]
def _buildBondedToAtomList(self, topology): def _buildBondedToAtomList(self, topology):
...@@ -2276,10 +2306,11 @@ class NonbondedGenerator(object): ...@@ -2276,10 +2306,11 @@ class NonbondedGenerator(object):
SCALETOL = 1e-5 SCALETOL = 1e-5
def __init__(self, forcefield, coulomb14scale, lj14scale): def __init__(self, forcefield, coulomb14scale, lj14scale, useDispersionCorrection):
self.ff = forcefield self.ff = forcefield
self.coulomb14scale = coulomb14scale self.coulomb14scale = coulomb14scale
self.lj14scale = lj14scale self.lj14scale = lj14scale
self.useDispersionCorrection = useDispersionCorrection
self.params = ForceField._AtomTypeParameters(forcefield, 'NonbondedForce', 'Atom', ('charge', 'sigma', 'epsilon')) self.params = ForceField._AtomTypeParameters(forcefield, 'NonbondedForce', 'Atom', ('charge', 'sigma', 'epsilon'))
def registerAtom(self, parameters): def registerAtom(self, parameters):
...@@ -2288,15 +2319,31 @@ class NonbondedGenerator(object): ...@@ -2288,15 +2319,31 @@ class NonbondedGenerator(object):
@staticmethod @staticmethod
def parseElement(element, ff): def parseElement(element, ff):
existing = [f for f in ff._forces if isinstance(f, NonbondedGenerator)] existing = [f for f in ff._forces if isinstance(f, NonbondedGenerator)]
if 'useDispersionCorrection' in element.attrib:
useDispersionCorrection = bool(eval(element.attrib.get('useDispersionCorrection')))
else:
useDispersionCorrection = None
if len(existing) == 0: if len(existing) == 0:
generator = NonbondedGenerator(ff, float(element.attrib['coulomb14scale']), float(element.attrib['lj14scale'])) generator = NonbondedGenerator(
ff,
float(element.attrib['coulomb14scale']),
float(element.attrib['lj14scale']),
useDispersionCorrection
)
ff.registerGenerator(generator) ff.registerGenerator(generator)
else: else:
# Multiple <NonbondedForce> tags were found, probably in different files. Simply add more types to the existing one. # Multiple <NonbondedForce> tags were found, probably in different files. Simply add more types to the existing one.
generator = existing[0] generator = existing[0]
if abs(generator.coulomb14scale - float(element.attrib['coulomb14scale'])) > NonbondedGenerator.SCALETOL or \ if (abs(generator.coulomb14scale - float(element.attrib['coulomb14scale'])) > NonbondedGenerator.SCALETOL
abs(generator.lj14scale - float(element.attrib['lj14scale'])) > NonbondedGenerator.SCALETOL: or abs(generator.lj14scale - float(element.attrib['lj14scale'])) > NonbondedGenerator.SCALETOL
):
raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales') raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales')
if (
generator.useDispersionCorrection is not None
and useDispersionCorrection is not None
and generator.useDispersionCorrection != useDispersionCorrection
):
raise ValueError('Found multiple NonbondedForce tags with different useDispersionCorrection settings.')
generator.params.parseDefinitions(element) generator.params.parseDefinitions(element)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
...@@ -2320,7 +2367,18 @@ class NonbondedGenerator(object): ...@@ -2320,7 +2367,18 @@ class NonbondedGenerator(object):
if 'ewaldErrorTolerance' in args: if 'ewaldErrorTolerance' in args:
force.setEwaldErrorTolerance(args['ewaldErrorTolerance']) force.setEwaldErrorTolerance(args['ewaldErrorTolerance'])
if 'useDispersionCorrection' in args: if 'useDispersionCorrection' in args:
force.setUseDispersionCorrection(bool(args['useDispersionCorrection'])) lrc_keyword = bool(args['useDispersionCorrection'])
if self.useDispersionCorrection is not None and lrc_keyword != self.useDispersionCorrection:
warnings.warn(
"Conflicting settings for useDispersionCorrection in createSystem() and forcefield file. "
"Using the one specified in createSystem()."
)
force.setUseDispersionCorrection(lrc_keyword)
elif self.useDispersionCorrection is not None:
force.setUseDispersionCorrection(self.useDispersionCorrection)
else:
# by default
force.setUseDispersionCorrection(True)
sys.addForce(force) sys.addForce(force)
def postprocessSystem(self, sys, data, args): def postprocessSystem(self, sys, data, args):
...@@ -2337,10 +2395,11 @@ parsers["NonbondedForce"] = NonbondedGenerator.parseElement ...@@ -2337,10 +2395,11 @@ parsers["NonbondedForce"] = NonbondedGenerator.parseElement
class LennardJonesGenerator(object): class LennardJonesGenerator(object):
"""A NBFix generator to construct the L-J force with NBFIX implemented as a lookup table""" """A NBFix generator to construct the L-J force with NBFIX implemented as a lookup table"""
def __init__(self, forcefield, lj14scale): def __init__(self, forcefield, lj14scale, useDispersionCorrection):
self.ff = forcefield self.ff = forcefield
self.nbfixTypes = {} self.nbfixTypes = {}
self.lj14scale = lj14scale self.lj14scale = lj14scale
self.useDispersionCorrection = useDispersionCorrection
self.ljTypes = ForceField._AtomTypeParameters(forcefield, 'LennardJonesForce', 'Atom', ('sigma', 'epsilon')) self.ljTypes = ForceField._AtomTypeParameters(forcefield, 'LennardJonesForce', 'Atom', ('sigma', 'epsilon'))
def registerNBFIX(self, parameters): def registerNBFIX(self, parameters):
...@@ -2359,14 +2418,28 @@ class LennardJonesGenerator(object): ...@@ -2359,14 +2418,28 @@ class LennardJonesGenerator(object):
@staticmethod @staticmethod
def parseElement(element, ff): def parseElement(element, ff):
existing = [f for f in ff._forces if isinstance(f, LennardJonesGenerator)] existing = [f for f in ff._forces if isinstance(f, LennardJonesGenerator)]
if 'useDispersionCorrection' in element.attrib:
useDispersionCorrection = bool(eval(element.attrib.get('useDispersionCorrection')))
else:
useDispersionCorrection = None
if len(existing) == 0: if len(existing) == 0:
generator = LennardJonesGenerator(ff, float(element.attrib['lj14scale'])) generator = LennardJonesGenerator(
ff,
float(element.attrib['lj14scale']),
useDispersionCorrection=useDispersionCorrection
)
ff.registerGenerator(generator) ff.registerGenerator(generator)
else: else:
# Multiple <LennardJonesForce> tags were found, probably in different files # Multiple <LennardJonesForce> tags were found, probably in different files
generator = existing[0] generator = existing[0]
if abs(generator.lj14scale - float(element.attrib['lj14scale'])) > NonbondedGenerator.SCALETOL: if abs(generator.lj14scale - float(element.attrib['lj14scale'])) > NonbondedGenerator.SCALETOL:
raise ValueError('Found multiple LennardJonesForce tags with different 1-4 scales') raise ValueError('Found multiple LennardJonesForce tags with different 1-4 scales')
if (
generator.useDispersionCorrection is not None
and useDispersionCorrection is not None
and generator.useDispersionCorrection != useDispersionCorrection
):
raise ValueError('Found multiple LennardJonesForce tags with different useDispersionCorrection settings.')
for LJ in element.findall('Atom'): for LJ in element.findall('Atom'):
generator.registerLennardJones(LJ.attrib) generator.registerLennardJones(LJ.attrib)
for Nbfix in element.findall('NBFixPair'): for Nbfix in element.findall('NBFixPair'):
...@@ -2437,12 +2510,24 @@ class LennardJonesGenerator(object): ...@@ -2437,12 +2510,24 @@ class LennardJonesGenerator(object):
if args['switchDistance'] is not None: if args['switchDistance'] is not None:
self.force.setUseSwitchingFunction(True) self.force.setUseSwitchingFunction(True)
self.force.setSwitchingDistance(args['switchDistance']) self.force.setSwitchingDistance(args['switchDistance'])
if 'useDispersionCorrection' in args:
lrc_keyword = bool(args['useDispersionCorrection'])
if self.useDispersionCorrection is not None and lrc_keyword != self.useDispersionCorrection:
warnings.warn(
"Conflicting settings for useDispersionCorrection in createSystem() and forcefield file. "
"Using the one specified in createSystem()."
)
self.force.setUseLongRangeCorrection(lrc_keyword)
elif self.useDispersionCorrection is not None:
self.force.setUseLongRangeCorrection(self.useDispersionCorrection)
else:
# by default
self.force.setUseLongRangeCorrection(True)
# Add the particles # Add the particles
for atom in data.atoms: for atom in data.atoms:
self.force.addParticle((typeToMergedType[data.atomType[atom]],)) self.force.addParticle((typeToMergedType[data.atomType[atom]],))
self.force.setUseLongRangeCorrection(True)
self.force.setCutoffDistance(nonbondedCutoff) self.force.setCutoffDistance(nonbondedCutoff)
sys.addForce(self.force) sys.addForce(self.force)
...@@ -2509,9 +2594,12 @@ class GBSAOBCGenerator(object): ...@@ -2509,9 +2594,12 @@ class GBSAOBCGenerator(object):
generator.params.parseDefinitions(element) generator.params.parseDefinitions(element)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff, methodMap = {NoCutoff:mm.GBSAOBCForce.NoCutoff,
CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic, CutoffNonPeriodic:mm.GBSAOBCForce.CutoffNonPeriodic,
CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic} CutoffPeriodic:mm.GBSAOBCForce.CutoffPeriodic,
Ewald:mm.GBSAOBCForce.CutoffPeriodic,
PME:mm.GBSAOBCForce.CutoffPeriodic,
LJPME:mm.GBSAOBCForce.CutoffPeriodic}
if nonbondedMethod not in methodMap: if nonbondedMethod not in methodMap:
raise ValueError('Illegal nonbonded method for GBSAOBCForce') raise ValueError('Illegal nonbonded method for GBSAOBCForce')
force = mm.GBSAOBCForce() force = mm.GBSAOBCForce()
...@@ -2746,7 +2834,10 @@ class CustomNonbondedGenerator(object): ...@@ -2746,7 +2834,10 @@ class CustomNonbondedGenerator(object):
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff, methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff,
CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic, CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic,
CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic} CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic,
Ewald:mm.CustomNonbondedForce.CutoffPeriodic,
PME:mm.CustomNonbondedForce.CutoffPeriodic,
LJPME:mm.CustomNonbondedForce.CutoffPeriodic}
if nonbondedMethod not in methodMap: if nonbondedMethod not in methodMap:
raise ValueError('Illegal nonbonded method for CustomNonbondedForce') raise ValueError('Illegal nonbonded method for CustomNonbondedForce')
force = mm.CustomNonbondedForce(self.energy) force = mm.CustomNonbondedForce(self.energy)
...@@ -2806,7 +2897,10 @@ class CustomGBGenerator(object): ...@@ -2806,7 +2897,10 @@ class CustomGBGenerator(object):
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomGBForce.NoCutoff, methodMap = {NoCutoff:mm.CustomGBForce.NoCutoff,
CutoffNonPeriodic:mm.CustomGBForce.CutoffNonPeriodic, CutoffNonPeriodic:mm.CustomGBForce.CutoffNonPeriodic,
CutoffPeriodic:mm.CustomGBForce.CutoffPeriodic} CutoffPeriodic:mm.CustomGBForce.CutoffPeriodic,
Ewald:mm.CustomGBForce.CutoffPeriodic,
PME:mm.CustomGBForce.CutoffPeriodic,
LJPME:mm.CustomGBForce.CutoffPeriodic}
if nonbondedMethod not in methodMap: if nonbondedMethod not in methodMap:
raise ValueError('Illegal nonbonded method for CustomGBForce') raise ValueError('Illegal nonbonded method for CustomGBForce')
force = mm.CustomGBForce() force = mm.CustomGBForce()
...@@ -2889,7 +2983,10 @@ class CustomHbondGenerator(object): ...@@ -2889,7 +2983,10 @@ class CustomHbondGenerator(object):
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomHbondForce.NoCutoff, methodMap = {NoCutoff:mm.CustomHbondForce.NoCutoff,
CutoffNonPeriodic:mm.CustomHbondForce.CutoffNonPeriodic, CutoffNonPeriodic:mm.CustomHbondForce.CutoffNonPeriodic,
CutoffPeriodic:mm.CustomHbondForce.CutoffPeriodic} CutoffPeriodic:mm.CustomHbondForce.CutoffPeriodic,
Ewald:mm.CustomHbondForce.CutoffPeriodic,
PME:mm.CustomHbondForce.CutoffPeriodic,
LJPME:mm.CustomHbondForce.CutoffPeriodic}
if nonbondedMethod not in methodMap: if nonbondedMethod not in methodMap:
raise ValueError('Illegal nonbonded method for CustomNonbondedForce') raise ValueError('Illegal nonbonded method for CustomNonbondedForce')
force = mm.CustomHbondForce(self.energy) force = mm.CustomHbondForce(self.energy)
...@@ -3027,7 +3124,10 @@ class CustomManyParticleGenerator(object): ...@@ -3027,7 +3124,10 @@ class CustomManyParticleGenerator(object):
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomManyParticleForce.NoCutoff, methodMap = {NoCutoff:mm.CustomManyParticleForce.NoCutoff,
CutoffNonPeriodic:mm.CustomManyParticleForce.CutoffNonPeriodic, CutoffNonPeriodic:mm.CustomManyParticleForce.CutoffNonPeriodic,
CutoffPeriodic:mm.CustomManyParticleForce.CutoffPeriodic} CutoffPeriodic:mm.CustomManyParticleForce.CutoffPeriodic,
Ewald:mm.CustomManyParticleForce.CutoffPeriodic,
PME:mm.CustomManyParticleForce.CutoffPeriodic,
LJPME:mm.CustomManyParticleForce.CutoffPeriodic}
if nonbondedMethod not in methodMap: if nonbondedMethod not in methodMap:
raise ValueError('Illegal nonbonded method for CustomManyParticleForce') raise ValueError('Illegal nonbonded method for CustomManyParticleForce')
force = mm.CustomManyParticleForce(self.particlesPerSet, self.energy) force = mm.CustomManyParticleForce(self.particlesPerSet, self.energy)
...@@ -4363,7 +4463,7 @@ class AmoebaVdwGenerator(object): ...@@ -4363,7 +4463,7 @@ class AmoebaVdwGenerator(object):
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
sigmaMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'CUBIC-MEAN':1} sigmaMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'CUBIC-MEAN':1}
epsilonMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'HARMONIC':1, 'HHG':1} epsilonMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'HARMONIC':1, 'W-H':1, 'HHG':1}
force = mm.AmoebaVdwForce() force = mm.AmoebaVdwForce()
sys.addForce(force) sys.addForce(force)
......
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ 8dd60914
...@@ -563,20 +563,27 @@ class GromacsTopFile(object): ...@@ -563,20 +563,27 @@ class GromacsTopFile(object):
if atomName in atomReplacements: if atomName in atomReplacements:
atomName = atomReplacements[atomName] atomName = atomReplacements[atomName]
# Try to guess the element. # Try to determine the element.
upper = atomName.upper() atomicNumber = self._atomTypes[fields[1]][2]
if upper.startswith('CL'): if atomicNumber is None:
element = elem.chlorine # Try to guess the element from the name.
elif upper.startswith('NA'): upper = atomName.upper()
element = elem.sodium if upper.startswith('CL'):
elif upper.startswith('MG'): element = elem.chlorine
element = elem.magnesium elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
elif atomicNumber == '0':
element = None
else: else:
try: element = elem.Element.getByAtomicNumber(int(atomicNumber))
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
atoms.append(top.addAtom(atomName, element, r)) atoms.append(top.addAtom(atomName, element, r))
# Add bonds to the topology # Add bonds to the topology
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 8dd60914
...@@ -989,6 +989,8 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No ...@@ -989,6 +989,8 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
gb = mm.GBSAOBCForce() gb = mm.GBSAOBCForce()
gb.setSoluteDielectric(soluteDielectric) gb.setSoluteDielectric(soluteDielectric)
gb.setSolventDielectric(solventDielectric) gb.setSolventDielectric(solventDielectric)
if gbsaModel is None:
gb.setSurfaceAreaEnergy(0)
elif gbmodel == 'GBn': elif gbmodel == 'GBn':
gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, gbsaModel, cutoff, implicitSolventKappa) gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, gbsaModel, cutoff, implicitSolventKappa)
elif gbmodel == 'GBn2': elif gbmodel == 'GBn2':
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 8dd60914
...@@ -250,7 +250,7 @@ def _bondi_radii(topology): ...@@ -250,7 +250,7 @@ def _bondi_radii(topology):
E.silicon: 2.1, E.silicon: 2.1,
E.phosphorus: 1.85, E.phosphorus: 1.85,
E.sulfur: 1.8, E.sulfur: 1.8,
E.chlorine: 1.5, E.chlorine: 1.7,
} }
if _have_numpy: if _have_numpy:
...@@ -272,7 +272,7 @@ def _mbondi_radii(topology, all_bonds = None): ...@@ -272,7 +272,7 @@ def _mbondi_radii(topology, all_bonds = None):
E.silicon: 2.1, E.silicon: 2.1,
E.phosphorus: 1.85, E.phosphorus: 1.85,
E.sulfur: 1.8, E.sulfur: 1.8,
E.chlorine: 1.5, E.chlorine: 1.7,
} }
if _have_numpy: if _have_numpy:
radii = numpy.empty(topology.getNumAtoms(), numpy.double) radii = numpy.empty(topology.getNumAtoms(), numpy.double)
...@@ -310,7 +310,7 @@ def _mbondi2_radii(topology, all_bonds = None): ...@@ -310,7 +310,7 @@ def _mbondi2_radii(topology, all_bonds = None):
E.silicon: 2.1, E.silicon: 2.1,
E.phosphorus: 1.85, E.phosphorus: 1.85,
E.sulfur: 1.8, E.sulfur: 1.8,
E.chlorine: 1.5, E.chlorine: 1.7,
} }
if _have_numpy: if _have_numpy:
radii = numpy.empty(topology.getNumAtoms(), numpy.double) radii = numpy.empty(topology.getNumAtoms(), numpy.double)
...@@ -389,18 +389,20 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k ...@@ -389,18 +389,20 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions) "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
_SCREEN_PARAMETERS = { # normal, GBn, GBn2 _SCREEN_PARAMETERS = { # normal, GBn, GBn2, GBn2 nucleic
E.hydrogen : (0.85, 1.09085413633, 1.425952), E.hydrogen : (0.85, 1.09085413633, 1.425952, 1.696538),
E.carbon : (0.72, 0.48435382330, 1.058554), E.carbon : (0.72, 0.48435382330, 1.058554, 1.268902),
E.nitrogen : (0.79, 0.700147318409, 0.733599), E.nitrogen : (0.79, 0.700147318409, 0.733599, 1.4259728),
E.oxygen : (0.85, 1.06557401132, 1.061039), E.oxygen : (0.85, 1.06557401132, 1.061039, 0.1840098),
E.fluorine : (0.88, 0.5, 0.5), E.fluorine : (0.88, 0.5, 0.5, 0.5),
E.phosphorus : (0.86, 0.5, 0.5), E.phosphorus : (0.86, 0.5, 0.5, 1.5450597),
E.sulfur : (0.96, 0.602256336067, -0.703469), E.sulfur : (0.96, 0.602256336067, -0.703469, 0.05),
None : (0.8, 0.5, 0.5) # default None : (0.8, 0.5, 0.5, 0.5) # default
} }
_SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen] _SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen]
_NUCLEIC_ACID_RESIDUES = ['A', 'C', 'G', 'U', 'DA', 'DC', 'DG', 'DT']
def _screen_parameter(atom): def _screen_parameter(atom):
return _SCREEN_PARAMETERS.get(atom.element, _SCREEN_PARAMETERS[None]) return _SCREEN_PARAMETERS.get(atom.element, _SCREEN_PARAMETERS[None])
...@@ -541,7 +543,7 @@ class GBSAHCTForce(CustomAmberGBForceBase): ...@@ -541,7 +543,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
self.addPerParticleParameter("charge") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" self.addComputedValue("I", "select(step(r+sr2-or1), 0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r), 0);"
"U=r+sr2;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2)", "D=abs(r-sr2)",
...@@ -607,7 +609,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase): ...@@ -607,7 +609,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
self.addPerParticleParameter("charge") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" self.addComputedValue("I", "select(step(r+sr2-or1), 0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r), 0);"
"U=r+sr2;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions) "D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
...@@ -675,7 +677,7 @@ class GBSAOBC2Force(GBSAOBC1Force): ...@@ -675,7 +677,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
self.addPerParticleParameter("charge") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" self.addComputedValue("I", "select(step(r+sr2-or1), 0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r), 0);"
"U=r+sr2;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions) "D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
...@@ -873,7 +875,16 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -873,7 +875,16 @@ class GBSAGBn2Force(GBSAGBnForce):
E.oxygen: [0.867814, 0.876635, 0.387882], E.oxygen: [0.867814, 0.876635, 0.387882],
E.sulfur: [0.867814, 0.876635, 0.387882], E.sulfur: [0.867814, 0.876635, 0.387882],
} }
_default_atom_params = [0.8, 4.85, 0.5] _atom_params_nucleic = {
E.hydrogen: [0.537050, 0.362861, 0.116704],
E.deuterium: [0.537050, 0.362861, 0.116704],
E.carbon: [0.331670, 0.196842, 0.093422],
E.nitrogen: [0.686311, 0.463189, 0.138722],
E.oxygen: [0.606344, 0.463006, 0.142262],
E.sulfur: [0.606344, 0.463006, 0.142262],
E.phosphorus: [0.418365, 0.290054, 0.1064245],
}
_default_atom_params = [1.0, 0.8, 4.851]
@classmethod @classmethod
def getStandardParameters(cls, topology): def getStandardParameters(cls, topology):
...@@ -897,14 +908,23 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -897,14 +908,23 @@ class GBSAGBn2Force(GBSAGBnForce):
radii = numpy.empty([natoms,5], numpy.double) radii = numpy.empty([natoms,5], numpy.double)
radii[:,0] = _mbondi3_radii(topology)/10 radii[:,0] = _mbondi3_radii(topology)/10
for atom, rad in zip(topology.atoms(), radii): for atom, rad in zip(topology.atoms(), radii):
rad[1] = _screen_parameter(atom)[2] if atom.residue.name in _NUCLEIC_ACID_RESIDUES:
rad[2:] = cls._atom_params.get(atom.element, cls._default_atom_params) rad[1] = _screen_parameter(atom)[3]
rad[2:] = cls._atom_params_nucleic.get(atom.element, cls._default_atom_params)
else:
rad[1] = _screen_parameter(atom)[2]
rad[2:] = cls._atom_params.get(atom.element, cls._default_atom_params)
else: else:
radii = [[r/10, 0, 0, 0, 0] for r in _mbondi3_radii(topology)] radii = [[r/10, 0, 0, 0, 0] for r in _mbondi3_radii(topology)]
for atom, rad in zip(topology.atoms(), radii): for atom, rad in zip(topology.atoms(), radii):
rad[1] = _screen_parameter(atom)[2] if atom.residue.name in _NUCLEIC_ACID_RESIDUES:
for i, p in enumerate(cls._atom_params.get(atom.element, cls._default_atom_params)): rad[1] = _screen_parameter(atom)[3]
rad[2+i] = p for i, p in enumerate(cls._atom_params_nucleic.get(atom.element, cls._default_atom_params)):
rad[2+i] = p
else:
rad[1] = _screen_parameter(atom)[2]
for i, p in enumerate(cls._atom_params.get(atom.element, cls._default_atom_params)):
rad[2+i] = p
return radii return radii
def _addEnergyTerms(self): def _addEnergyTerms(self):
......
wrappers/python/simtk/openmm/app/metadynamics.py 0 → 100644
View file @ 8dd60914
"""
metadynamics.py: Well-tempered metadynamics
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2018-2019 Stanford University and the Authors.
Authors: Peter Eastman
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import simtk.openmm as mm
import simtk.unit as unit
from collections import namedtuple
from functools import reduce
import os
import re
try:
import numpy as np
except:
pass
class Metadynamics(object):
"""Performs metadynamics.
This class implements well-tempered metadynamics, as described in Barducci et al.,
"Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method"
(https://doi.org/10.1103/PhysRevLett.100.020603). You specify from one to three
collective variables whose sampling should be accelerated. A biasing force that
depends on the collective variables is added to the simulation. Initially the bias
is zero. As the simulation runs, Gaussian bumps are periodically added to the bias
at the current location of the simulation. This pushes the simulation away from areas
it has already explored, encouraging it to sample other regions. At the end of the
simulation, the bias function can be used to calculate the system's free energy as a
function of the collective variables.
To use the class you create a Metadynamics object, passing to it the System you want
to simulate and a list of BiasVariable objects defining the collective variables.
It creates a biasing force and adds it to the System. You then run the simulation
as usual, but call step() on the Metadynamics object instead of on the Simulation.
You can optionally specify a directory on disk where the current bias function should
periodically be written. In addition, it loads biases from any other files in the
same directory and includes them in the simulation. It loads files when the
Metqdynamics object is first created, and also checks for any new files every time it
updates its own bias on disk.
This serves two important functions. First, it lets you stop a metadynamics run and
resume it later. When you begin the new simulation, it will load the biases computed
in the earlier simulation and continue adding to them. Second, it provides an easy
way to parallelize metadynamics sampling across many computers. Just point all of
them to a shared directory on disk. Each process will save its biases to that
directory, and also load in and apply the biases added by other processes.
"""
def __init__(self, system, variables, temperature, biasFactor, height, frequency, saveFrequency=None, biasDir=None):
"""Create a Metadynamics object.
Parameters
----------
system: System
the System to simulate. A CustomCVForce implementing the bias is created and
added to the System.
variables: list of BiasVariables
the collective variables to sample
temperature: temperature
the temperature at which the simulation is being run. This is used in computing
the free energy.
biasFactor: float
used in scaling the height of the Gaussians added to the bias. The collective
variables are sampled as if the effective temperature of the simulation were
temperature*biasFactor.
height: energy
the initial height of the Gaussians to add
frequency: int
the interval in time steps at which Gaussians should be added to the bias potential
saveFrequency: int (optional)
the interval in time steps at which to write out the current biases to disk. At
the same time it writes biases, it also checks for updated biases written by other
processes and loads them in. This must be a multiple of frequency.
biasDir: str (optional)
the directory to which biases should be written, and from which biases written by
other processes should be loaded
"""
if not unit.is_quantity(temperature):
temperature = temperature*unit.kelvin
if not unit.is_quantity(height):
height = height*unit.kilojoules_per_mole
if biasFactor < 1.0:
raise ValueError('biasFactor must be >= 1')
if (saveFrequency is None and biasDir is not None) or (saveFrequency is not None and biasDir is None):
raise ValueError('Must specify both saveFrequency and biasDir')
if saveFrequency is not None and (saveFrequency < frequency or saveFrequency%frequency != 0):
raise ValueError('saveFrequency must be a multiple of frequency')
self.variables = variables
self.temperature = temperature
self.biasFactor = biasFactor
self.height = height
self.frequency = frequency
self.biasDir = biasDir
self.saveFrequency = saveFrequency
self._id = np.random.randint(0x7FFFFFFF)
self._saveIndex = 0
self._selfBias = np.zeros(tuple(v.gridWidth for v in variables))
self._totalBias = np.zeros(tuple(v.gridWidth for v in variables))
self._loadedBiases = {}
self._deltaT = temperature*(biasFactor-1)
varNames = ['cv%d' % i for i in range(len(variables))]
self._force = mm.CustomCVForce('table(%s)' % ', '.join(varNames))
for name, var in zip(varNames, variables):
self._force.addCollectiveVariable(name, var.force)
widths = [v.gridWidth for v in variables]
mins = [v.minValue for v in variables]
maxs = [v.maxValue for v in variables]
if len(variables) == 1:
self._table = mm.Continuous1DFunction(self._totalBias.flatten(), mins[0], maxs[0])
elif len(variables) == 2:
self._table = mm.Continuous2DFunction(widths[0], widths[1], self._totalBias.flatten(), mins[0], maxs[0], mins[1], maxs[1])
elif len(variables) == 3:
self._table = mm.Continuous3DFunction(widths[0], widths[1], widths[2], self._totalBias.flatten(), mins[0], maxs[0], mins[1], maxs[1], mins[2], maxs[2])
else:
raise ValueError('Metadynamics requires 1, 2, or 3 collective variables')
self._force.addTabulatedFunction('table', self._table)
self._force.setForceGroup(31)
system.addForce(self._force)
self._syncWithDisk()
def step(self, simulation, steps):
"""Advance the simulation by integrating a specified number of time steps.
Parameters
----------
simulation: Simulation
the Simulation to advance
steps: int
the number of time steps to integrate
"""
stepsToGo = steps
while stepsToGo > 0:
nextSteps = stepsToGo
if simulation.currentStep % self.frequency == 0:
nextSteps = min(nextSteps, self.frequency)
else:
nextSteps = min(nextSteps, simulation.currentStep % self.frequency)
simulation.step(nextSteps)
if simulation.currentStep % self.frequency == 0:
position = self._force.getCollectiveVariableValues(simulation.context)
energy = simulation.context.getState(getEnergy=True, groups={31}).getPotentialEnergy()
height = self.height*np.exp(-energy/(unit.MOLAR_GAS_CONSTANT_R*self._deltaT))
self._addGaussian(position, height, simulation.context)
if self.saveFrequency is not None and simulation.currentStep % self.saveFrequency == 0:
self._syncWithDisk()
stepsToGo -= nextSteps
def getFreeEnergy(self):
"""Get the free energy of the system as a function of the collective variables.
The result is returned as a N-dimensional NumPy array, where N is the number of collective
variables. The values are in kJ/mole. The i'th position along an axis corresponds to
minValue + i*(maxValue-minValue)/gridWidth.
"""
return -((self.temperature+self._deltaT)/self._deltaT)*self._totalBias*unit.kilojoules_per_mole
def getCollectiveVariables(self, simulation):
"""Get the current values of all collective variables in a Simulation."""
return self._force.getCollectiveVariableValues(simulation.context)
def _addGaussian(self, position, height, context):
"""Add a Gaussian to the bias function."""
# Compute a Gaussian along each axis.
axisGaussians = []
for i,v in enumerate(self.variables):
x = (position[i]-v.minValue) / (v.maxValue-v.minValue)
if v.periodic:
x = x % 1.0
dist = np.abs(np.linspace(0, 1.0, num=v.gridWidth) - x)
if v.periodic:
dist = np.min(np.array([dist, np.abs(dist-1)]), axis=0)
axisGaussians.append(np.exp(-dist*dist*v.gridWidth/v.biasWidth))
# Compute their outer product.
if len(self.variables) == 1:
gaussian = axisGaussians[0]
else:
gaussian = reduce(np.multiply.outer, reversed(axisGaussians))
# Add it to the bias.
height = height.value_in_unit(unit.kilojoules_per_mole)
self._selfBias += height*gaussian
self._totalBias += height*gaussian
widths = [v.gridWidth for v in self.variables]
mins = [v.minValue for v in self.variables]
maxs = [v.maxValue for v in self.variables]
if len(self.variables) == 1:
self._table.setFunctionParameters(self._totalBias.flatten(), mins[0], maxs[0])
elif len(self.variables) == 2:
self._table.setFunctionParameters(widths[0], widths[1], self._totalBias.flatten(), mins[0], maxs[0], mins[1], maxs[1])
elif len(self.variables) == 3:
self._table.setFunctionParameters(widths[0], widths[1], widths[2], self._totalBias.flatten(), mins[0], maxs[0], mins[1], maxs[1], mins[2], maxs[2])
self._force.updateParametersInContext(context)
def _syncWithDisk(self):
"""Save biases to disk, and check for updated files created by other processes."""
if self.biasDir is None:
return
# Use a safe save to write out the biases to disk, then delete the older file.
oldName = os.path.join(self.biasDir, 'bias_%d_%d.npy' % (self._id, self._saveIndex))
self._saveIndex += 1
tempName = os.path.join(self.biasDir, 'temp_%d_%d.npy' % (self._id, self._saveIndex))
fileName = os.path.join(self.biasDir, 'bias_%d_%d.npy' % (self._id, self._saveIndex))
np.save(tempName, self._selfBias)
os.rename(tempName, fileName)
if os.path.exists(oldName):
os.remove(oldName)
# Check for any files updated by other processes.
fileLoaded = False
pattern = re.compile('bias_(.*)_(.*)\.npy')
for filename in os.listdir(self.biasDir):
match = pattern.match(filename)
if match is not None:
matchId = int(match.group(1))
matchIndex = int(match.group(2))
if matchId != self._id and (matchId not in self._loadedBiases or matchIndex > self._loadedBiases[matchId].index):
try:
data = np.load(os.path.join(self.biasDir, filename))
self._loadedBiases[matchId] = _LoadedBias(matchId, matchIndex, data)
fileLoaded = True
except IOError:
# There's a tiny chance the file could get deleted by another process between when
# we check the directory and when we try to load it. If so, just ignore the error
# and keep using whatever version of that process' biases we last loaded.
pass
# If we loaded any files, recompute the total bias from all processes.
if fileLoaded:
self._totalBias = self._selfBias
for bias in self._loadedBiases.values():
self._totalBias += bias.bias
class BiasVariable(object):
"""A collective variable that can be used to bias a simulation with metadynamics."""
def __init__(self, force, minValue, maxValue, biasWidth, periodic=False, gridWidth=None):
"""Create a BiasVariable.
Parameters
----------
force: Force
the Force object whose potential energy defines the collective variable
minValue: float
the minimum value the collective variable can take. If it should ever go below this,
the bias force will be set to 0.
maxValue: float
the maximum value the collective variable can take. If it should ever go above this,
the bias force will be set to 0.
biasWidth: float
the width (standard deviation) of the Gaussians added to the bias during metadynamics
periodic: bool
whether this is a periodic variable, such that minValue and maxValue are physical equivalent
gridWidth: int
the number of grid points to use when tabulating the bias function. If this is omitted,
a reasonable value is chosen automatically.
"""
self.force = force
self.minValue = minValue
self.maxValue = maxValue
self.biasWidth = biasWidth
self.periodic = periodic
if gridWidth is None:
self.gridWidth = int(np.ceil(5*(maxValue-minValue)/biasWidth))
else:
self.gridWidth = gridWidth
_LoadedBias = namedtuple('LoadedBias', ['id', 'index', 'bias'])
wrappers/python/simtk/openmm/app/modeller.py
View file @ 8dd60914
...@@ -258,13 +258,16 @@ class Modeller(object): ...@@ -258,13 +258,16 @@ class Modeller(object):
self.topology = newTopology self.topology = newTopology
self.positions = newPositions self.positions = newPositions
def _addIons(self, forcefield, replaceableMols, ionCutoff=0.05*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True): def _addIons(self, forcefield, numWaters, replaceableMols, ionCutoff=0.05*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
"""Adds ions to the system by replacing certain molecules. """Adds ions to the system by replacing certain molecules.
Parameters Parameters
---------- ----------
forcefield : ForceField forcefield : ForceField
the ForceField to use to determine the total charge of the system. the ForceField to use to determine the total charge of the system.
numWaters : int
the total number of water molecules in the simulation box, used to
calculate the number of ions / concentration to add.
replaceableMols : dict replaceableMols : dict
the molecules to replace by ions, as a dictionary of residue:positions the molecules to replace by ions, as a dictionary of residue:positions
ionCutoff: distance=0.5*nanometer ionCutoff: distance=0.5*nanometer
...@@ -326,51 +329,52 @@ class Modeller(object): ...@@ -326,51 +329,52 @@ class Modeller(object):
numPositive -= totalCharge numPositive -= totalCharge
if ionicStrength > 0 * molar: if ionicStrength > 0 * molar:
numIons = (numReplaceableMols - numPositive - numNegative) * ionicStrength / (55.4 * molar) # Pure water is about 55.4 molar (depending on temperature) numIons = (numWaters - numPositive - numNegative) * ionicStrength / (55.4 * molar) # Pure water is about 55.4 molar (depending on temperature)
numPairs = int(floor(numIons + 0.5)) numPairs = int(floor(numIons + 0.5))
numPositive += numPairs numPositive += numPairs
numNegative += numPairs numNegative += numPairs
totalIons = numPositive + numNegative totalIons = numPositive + numNegative
# Randomly select a set of waters if totalIons > 0:
# while ensuring ions are not placed too close to each other. # Randomly select a set of waters
modeller = Modeller(self.topology, self.positions) # while ensuring ions are not placed too close to each other.
modeller = Modeller(self.topology, self.positions)
replaceableList = list(replaceableMols.keys())
numAddedIons = 0 replaceableList = list(replaceableMols.keys())
numTrials = 10 # Attempts to add ions N times before quitting numAddedIons = 0
toReplace = [] # list of molecules to be replaced numTrials = 10 # Attempts to add ions N times before quitting
while numAddedIons < totalIons: toReplace = [] # list of molecules to be replaced
pickedMol = random.choice(replaceableList) while numAddedIons < totalIons:
replaceableList.remove(pickedMol) pickedMol = random.choice(replaceableList)
# Check distance to other ions replaceableList.remove(pickedMol)
for pos in ionPositions: # Check distance to other ions
distance = norm(pos - replaceableMols[pickedMol]) for pos in ionPositions:
if distance <= ionCutoff: distance = norm(pos - replaceableMols[pickedMol])
numTrials -= 1 if distance <= ionCutoff:
break numTrials -= 1
else: break
toReplace.append(pickedMol) else:
ionPositions.append(replaceableMols[pickedMol]) toReplace.append(pickedMol)
numAddedIons += 1 ionPositions.append(replaceableMols[pickedMol])
numAddedIons += 1
n_trials = 10 n_trials = 10
if n_trials == 0: if n_trials == 0:
raise ValueError('Could not add more than {} ions to the system'.format(numAddedIons)) raise ValueError('Could not add more than {} ions to the system'.format(numAddedIons))
# Replace waters/ions in the topology # Replace waters/ions in the topology
modeller.delete(toReplace) modeller.delete(toReplace)
ionChain = modeller.topology.addChain() ionChain = modeller.topology.addChain()
for i, water in enumerate(toReplace): for i, water in enumerate(toReplace):
element = (positiveElement if i < numPositive else negativeElement) element = (positiveElement if i < numPositive else negativeElement)
newResidue = modeller.topology.addResidue(element.symbol.upper(), ionChain) newResidue = modeller.topology.addResidue(element.symbol.upper(), ionChain)
modeller.topology.addAtom(element.symbol, element, newResidue) modeller.topology.addAtom(element.symbol, element, newResidue)
modeller.positions.append(replaceableMols[water]) modeller.positions.append(replaceableMols[water])
# Update topology/positions # Update topology/positions
self.topology = modeller.topology self.topology = modeller.topology
self.positions = modeller.positions self.positions = modeller.positions
def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, numAdded=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True): def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, numAdded=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
"""Add solvent (both water and ions) to the model to fill a rectangular box. """Add solvent (both water and ions) to the model to fill a rectangular box.
...@@ -621,8 +625,11 @@ class Modeller(object): ...@@ -621,8 +625,11 @@ class Modeller(object):
if atom.element == _oxygen: if atom.element == _oxygen:
waterPos[residue] = newPositions[atom.index] waterPos[residue] = newPositions[atom.index]
# Total number of waters in the box
numTotalWaters = len(waterPos)
# Add ions to neutralize the system. # Add ions to neutralize the system.
self._addIons(forcefield, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize) self._addIons(forcefield, numTotalWaters, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize)
class _ResidueData: class _ResidueData:
"""Inner class used to encapsulate data about the hydrogens for a residue.""" """Inner class used to encapsulate data about the hydrogens for a residue."""
...@@ -712,6 +719,8 @@ class Modeller(object): ...@@ -712,6 +719,8 @@ class Modeller(object):
automatically, this function will only add hydrogens. It will never remove ones that are already present in the automatically, this function will only add hydrogens. It will never remove ones that are already present in the
model, regardless of the specified pH. model, regardless of the specified pH.
In all cases, the positions of existing atoms (including existing hydrogens) are not modified.
Definitions for standard amino acids and nucleotides are built in. You can call loadHydrogenDefinitions() to load Definitions for standard amino acids and nucleotides are built in. You can call loadHydrogenDefinitions() to load
additional definitions for other residue types. additional definitions for other residue types.
...@@ -930,14 +939,16 @@ class Modeller(object): ...@@ -930,14 +939,16 @@ class Modeller(object):
# The hydrogens were added at random positions. Now perform an energy minimization to fix them up. # The hydrogens were added at random positions. Now perform an energy minimization to fix them up.
addedH = set(newIndices) # keep track of Hs added
if forcefield is not None: if forcefield is not None:
# Use the ForceField the user specified. # Use the ForceField the user specified.
system = forcefield.createSystem(newTopology, rigidWater=False, nonbondedMethod=CutoffNonPeriodic) system = forcefield.createSystem(newTopology, rigidWater=False, nonbondedMethod=CutoffNonPeriodic)
atoms = list(newTopology.atoms()) atoms = list(newTopology.atoms())
for i in range(system.getNumParticles()): for i in range(system.getNumParticles()):
if atoms[i].element != elem.hydrogen: if i not in addedH:
# This is a heavy atom, so make it immobile. # Existing atom, make it immobile.
system.setParticleMass(i, 0) system.setParticleMass(i, 0)
else: else:
# Create a System that restrains the distance of each hydrogen from its parent atom # Create a System that restrains the distance of each hydrogen from its parent atom
...@@ -955,7 +966,7 @@ class Modeller(object): ...@@ -955,7 +966,7 @@ class Modeller(object):
bondedTo = [] bondedTo = []
for atom in newTopology.atoms(): for atom in newTopology.atoms():
nonbonded.addParticle([]) nonbonded.addParticle([])
if atom.element != elem.hydrogen: if atom.index not in addedH: # make immobile
system.addParticle(0.0) system.addParticle(0.0)
else: else:
system.addParticle(1.0) system.addParticle(1.0)
...@@ -1221,33 +1232,33 @@ class Modeller(object): ...@@ -1221,33 +1232,33 @@ class Modeller(object):
def addMembrane(self, forcefield, lipidType='POPC', membraneCenterZ=0*nanometer, minimumPadding=1*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True): def addMembrane(self, forcefield, lipidType='POPC', membraneCenterZ=0*nanometer, minimumPadding=1*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
"""Add a lipid membrane to the model. """Add a lipid membrane to the model.
This method actually adds both a membrane and a water box. It is best to build them together, This method actually adds both a membrane and a water box. It is best to build them together,
both to avoid adding waters inside the membrane and to ensure that lipid head groups are properly both to avoid adding waters inside the membrane and to ensure that lipid head groups are properly
solvated. For that reason, this method includes many of the same arguments as addSolvent(). solvated. For that reason, this method includes many of the same arguments as addSolvent().
The membrane is added in the XY plane, and the existing protein is assumed to already be oriented The membrane is added in the XY plane, and the existing protein is assumed to already be oriented
and positioned correctly. When possible, it is recommended to start with a model from the and positioned correctly. When possible, it is recommended to start with a model from the
Orientations of Proteins in Membranes (OPM) database at http://opm.phar.umich.edu. Otherwise, it Orientations of Proteins in Membranes (OPM) database at http://opm.phar.umich.edu. Otherwise, it
is up to you to select the protein position yourself. is up to you to select the protein position yourself.
The algorithm is based on the one described in Wolf et al., J. Comp. Chem. 31, pp. 2169-2174 (2010). The algorithm is based on the one described in Wolf et al., J. Comp. Chem. 31, pp. 2169-2174 (2010).
It begins by tiling copies of a pre-equilibrated membrane patch to create a membrane of the desired It begins by tiling copies of a pre-equilibrated membrane patch to create a membrane of the desired
size. Next it scales down the protein by 50% along the X and Y axes. Any lipid within a cutoff size. Next it scales down the protein by 50% along the X and Y axes. Any lipid within a cutoff
distance of the scaled protein is removed. It also ensures that equal numbers of lipids are removed distance of the scaled protein is removed. It also ensures that equal numbers of lipids are removed
from each leaf of the membrane. Finally, 1000 steps of molecular dynamics are performed to let from each leaf of the membrane. Finally, 1000 steps of molecular dynamics are performed to let
the membrane relax while the protein is gradually scaled back up to its original size. the membrane relax while the protein is gradually scaled back up to its original size.
The size of the membrane and water box are determined by the minimumPadding argument. All The size of the membrane and water box are determined by the minimumPadding argument. All
pre-existing atoms are guaranteed to be at least this far from any edge of the periodic box. It pre-existing atoms are guaranteed to be at least this far from any edge of the periodic box. It
is also possible for the periodic box to have more padding than requested. In particular, it only is also possible for the periodic box to have more padding than requested. In particular, it only
adds whole copies of the pre-equilibrated membrane patch, so the box dimensions will always be adds whole copies of the pre-equilibrated membrane patch, so the box dimensions will always be
integer multiples of the patch size. That may lead to a larger membrane than what you requested. integer multiples of the patch size. That may lead to a larger membrane than what you requested.
This method has built in support for POPC and POPE lipids. You can also build other types of This method has built in support for POPC and POPE lipids. You can also build other types of
membranes by providing a pre-equilibrated, solvated membrane patch that can be tiled in the XY membranes by providing a pre-equilibrated, solvated membrane patch that can be tiled in the XY
plane to form the membrane. plane to form the membrane.
Parameters Parameters
---------- ----------
forcefield : ForceField forcefield : ForceField
...@@ -1282,8 +1293,8 @@ class Modeller(object): ...@@ -1282,8 +1293,8 @@ class Modeller(object):
membraneCenterZ = membraneCenterZ.value_in_unit(nanometer) membraneCenterZ = membraneCenterZ.value_in_unit(nanometer)
if is_quantity(minimumPadding): if is_quantity(minimumPadding):
minimumPadding = minimumPadding.value_in_unit(nanometer) minimumPadding = minimumPadding.value_in_unit(nanometer)
# Figure out how many copies of the membrane patch we need in each direction. # Figure out how many copies of the membrane patch we need in each direction.
proteinPos = self.positions.value_in_unit(nanometer) proteinPos = self.positions.value_in_unit(nanometer)
proteinMinPos = Vec3(*[min((p[i] for p in proteinPos)) for i in range(3)]) proteinMinPos = Vec3(*[min((p[i] for p in proteinPos)) for i in range(3)])
...@@ -1298,15 +1309,15 @@ class Modeller(object): ...@@ -1298,15 +1309,15 @@ class Modeller(object):
patchCenterPos = (patchMinPos+patchMaxPos)/2 patchCenterPos = (patchMinPos+patchMaxPos)/2
nx = int(ceil((proteinSize[0]+2*minimumPadding)/patchSize[0])) nx = int(ceil((proteinSize[0]+2*minimumPadding)/patchSize[0]))
ny = int(ceil((proteinSize[1]+2*minimumPadding)/patchSize[1])) ny = int(ceil((proteinSize[1]+2*minimumPadding)/patchSize[1]))
# Record the bonds for each residue. # Record the bonds for each residue.
resBonds = defaultdict(list) resBonds = defaultdict(list)
for bond in patch.topology.bonds(): for bond in patch.topology.bonds():
resBonds[bond[0].residue].append(bond) resBonds[bond[0].residue].append(bond)
# Identify which leaf of the membrane each lipid is in. # Identify which leaf of the membrane each lipid is in.
numLipidAtoms = 0 numLipidAtoms = 0
resMeanZ = {} resMeanZ = {}
membraneMeanZ = 0.0 membraneMeanZ = 0.0
...@@ -1322,17 +1333,17 @@ class Modeller(object): ...@@ -1322,17 +1333,17 @@ class Modeller(object):
resMeanZ[res] = sumZ/numResAtoms resMeanZ[res] = sumZ/numResAtoms
membraneMeanZ /= numLipidAtoms membraneMeanZ /= numLipidAtoms
lipidLeaf = dict((res, 0 if resMeanZ[res] < membraneMeanZ else 1) for res in resMeanZ) lipidLeaf = dict((res, 0 if resMeanZ[res] < membraneMeanZ else 1) for res in resMeanZ)
# Compute scaled positions for the protein. # Compute scaled positions for the protein.
scaledProteinPos = [None]*len(proteinPos) scaledProteinPos = [None]*len(proteinPos)
for i, p in enumerate(proteinPos): for i, p in enumerate(proteinPos):
p = p-proteinCenterPos p = p-proteinCenterPos
p = Vec3(0.5*p[0], 0.5*p[1], p[2]) p = Vec3(0.5*p[0], 0.5*p[1], p[2])
scaledProteinPos[i] = p+proteinCenterPos scaledProteinPos[i] = p+proteinCenterPos
# Create a new Topology for the membrane. # Create a new Topology for the membrane.
membraneTopology = Topology() membraneTopology = Topology()
membranePos = [] membranePos = []
boxSizeZ = patchSize[2] boxSizeZ = patchSize[2]
...@@ -1341,14 +1352,13 @@ class Modeller(object): ...@@ -1341,14 +1352,13 @@ class Modeller(object):
else: else:
boxSizeZ = max(boxSizeZ, proteinSize[2]+2*minimumPadding) boxSizeZ = max(boxSizeZ, proteinSize[2]+2*minimumPadding)
membraneTopology.setUnitCellDimensions((nx*patchSize[0], ny*patchSize[1], boxSizeZ)) membraneTopology.setUnitCellDimensions((nx*patchSize[0], ny*patchSize[1], boxSizeZ))
# Add membrane patches. We exclude any water that is within a cutoff distance of either the actual or scaled # Add membrane patches. We exclude any water that is within a cutoff distance of either the actual or scaled
# protein, and any lipid that is within a cutoff distance of the scaled protein. We also keep track of how # protein, and any lipid that is within a cutoff distance of the scaled protein. We also keep track of how
# many lipids have been excluded from each leaf of the membrane, so we can make sure exactly the same # many lipids have been excluded from each leaf of the membrane, so we can make sure exactly the same
# number get removed from each leaf. # number get removed from each leaf.
overlapCutoff = 0.22 overlapCutoff = 0.22
chain = membraneTopology.addChain()
addedWater = [] addedWater = []
addedLipids = [] addedLipids = []
removedFromLeaf = [0, 0] removedFromLeaf = [0, 0]
...@@ -1395,28 +1405,32 @@ class Modeller(object): ...@@ -1395,28 +1405,32 @@ class Modeller(object):
del cellLists del cellLists
del cells del cells
del proteinCells del proteinCells
# Add the lipids. # Add the lipids.
newAtoms = {} newAtoms = {}
lipidChain = membraneTopology.addChain() lipidChain = membraneTopology.addChain()
lipidResNum = 1 # renumber lipid residues to handle large patches
for (nearest, residue, pos) in addedLipids: for (nearest, residue, pos) in addedLipids:
if skipFromLeaf[lipidLeaf[residue]] > 0: if skipFromLeaf[lipidLeaf[residue]] > 0:
# Remove the same number of residues from each leaf. # Remove the same number of residues from each leaf.
skipFromLeaf[lipidLeaf[residue]] -= 1 skipFromLeaf[lipidLeaf[residue]] -= 1
else: else:
newResidue = membraneTopology.addResidue(residue.name, lipidChain, residue.id, residue.insertionCode) newResidue = membraneTopology.addResidue(residue.name, lipidChain, lipidResNum, residue.insertionCode)
lipidResNum += 1
for atom in residue.atoms(): for atom in residue.atoms():
newAtom = membraneTopology.addAtom(atom.name, atom.element, newResidue, atom.id) newAtom = membraneTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
newAtoms[atom] = newAtom newAtoms[atom] = newAtom
membranePos += pos membranePos += pos
for bond in resBonds[residue]: for bond in resBonds[residue]:
membraneTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]], bond.type, bond.order) membraneTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]], bond.type, bond.order)
del lipidLeaf del lipidLeaf
del addedLipids del addedLipids
# Add the solvent. # Add the solvent.
solventChain = membraneTopology.addChain() solventChain = membraneTopology.addChain()
for (residue, pos) in addedWater: for (residue, pos) in addedWater:
newResidue = membraneTopology.addResidue(residue.name, solventChain, residue.id, residue.insertionCode) newResidue = membraneTopology.addResidue(residue.name, solventChain, residue.id, residue.insertionCode)
...@@ -1432,7 +1446,7 @@ class Modeller(object): ...@@ -1432,7 +1446,7 @@ class Modeller(object):
gc.collect() gc.collect()
# Create a System for the lipids, then add in the protein as stationary particles. # Create a System for the lipids, then add in the protein as stationary particles.
system = forcefield.createSystem(membraneTopology, nonbondedMethod=CutoffPeriodic) system = forcefield.createSystem(membraneTopology, nonbondedMethod=CutoffPeriodic)
proteinSystem = forcefield.createSystem(self.topology, nonbondedMethod=CutoffNonPeriodic) proteinSystem = forcefield.createSystem(self.topology, nonbondedMethod=CutoffNonPeriodic)
numMembraneParticles = system.getNumParticles() numMembraneParticles = system.getNumParticles()
...@@ -1454,9 +1468,9 @@ class Modeller(object): ...@@ -1454,9 +1468,9 @@ class Modeller(object):
del membranePos del membranePos
del scaledProteinCells del scaledProteinCells
gc.collect() gc.collect()
# Run a simulation while slowly scaling up the protein so the membrane can relax. # Run a simulation while slowly scaling up the protein so the membrane can relax.
integrator = LangevinIntegrator(10.0, 50.0, 0.001) integrator = LangevinIntegrator(10.0, 50.0, 0.001)
context = Context(system, integrator) context = Context(system, integrator)
context.setPositions(mergedPositions) context.setPositions(mergedPositions)
...@@ -1479,24 +1493,24 @@ class Modeller(object): ...@@ -1479,24 +1493,24 @@ class Modeller(object):
mergedPositions[j+numMembraneParticles] = (weight1*proteinPos[j] + weight2*scaledProteinPos[j]) mergedPositions[j+numMembraneParticles] = (weight1*proteinPos[j] + weight2*scaledProteinPos[j])
context.setPositions(mergedPositions) context.setPositions(mergedPositions)
integrator.step(20) integrator.step(20)
# Add the membrane to the protein. # Add the membrane to the protein.
modeller = Modeller(self.topology, self.positions) modeller = Modeller(self.topology, self.positions)
modeller.add(membraneTopology, context.getState(getPositions=True).getPositions()[:numMembraneParticles]) modeller.add(membraneTopology, context.getState(getPositions=True).getPositions()[:numMembraneParticles])
modeller.topology.setPeriodicBoxVectors(membraneTopology.getPeriodicBoxVectors()) modeller.topology.setPeriodicBoxVectors(membraneTopology.getPeriodicBoxVectors())
del context del context
del system del system
del integrator del integrator
# Depending on the box size, we may need to add more water beyond what was included with the membrane patch. # Depending on the box size, we may need to add more water beyond what was included with the membrane patch.
needExtraWater = (boxSizeZ > patchSize[2]) needExtraWater = (boxSizeZ > patchSize[2])
if needExtraWater: if needExtraWater:
modeller.addSolvent(forcefield, neutralize=False) modeller.addSolvent(forcefield, neutralize=False)
# Record the positions of all waters that have been added. # Record the positions of all waters that have been added.
waterPos = {} waterPos = {}
for chain in list(modeller.topology.chains())[-2:]: for chain in list(modeller.topology.chains())[-2:]:
for residue in chain.residues(): for residue in chain.residues():
...@@ -1534,6 +1548,11 @@ class Modeller(object): ...@@ -1534,6 +1548,11 @@ class Modeller(object):
if atom.element == elem.oxygen: if atom.element == elem.oxygen:
waterPos[residue] = modeller.positions[atom.index] waterPos[residue] = modeller.positions[atom.index]
# Total number of water molecules
# Use this number to avoid underestimating the concentration of ions
# in _addIons after we exclude waters close to lipids.
numTotalWaters = len(waterPos)
# Calculate lipid Z boundaries # Calculate lipid Z boundaries
lipidNames = {res.name for res in patch.topology.residues() if res.name != 'HOH'} lipidNames = {res.name for res in patch.topology.residues() if res.name != 'HOH'}
lipidZMax = sys.float_info.min lipidZMax = sys.float_info.min
...@@ -1555,12 +1574,12 @@ class Modeller(object): ...@@ -1555,12 +1574,12 @@ class Modeller(object):
if lowerZBoundary < waterZ.value_in_unit(nanometer) < upperZBoundary: if lowerZBoundary < waterZ.value_in_unit(nanometer) < upperZBoundary:
del waterPos[wRes] del waterPos[wRes]
self._addIons(forcefield, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize) self._addIons(forcefield, numTotalWaters, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize)
class _CellList(object): class _CellList(object):
"""This class organizes atom positions into cells, so the neighbors of a point can be quickly retrieved""" """This class organizes atom positions into cells, so the neighbors of a point can be quickly retrieved"""
def __init__(self, positions, maxCutoff, vectors, periodic): def __init__(self, positions, maxCutoff, vectors, periodic):
self.positions = positions[:] self.positions = positions[:]
self.cells = {} self.cells = {}
......
wrappers/python/simtk/openmm/app/pdbfile.py
View file @ 8dd60914
...@@ -69,8 +69,8 @@ class PDBFile(object): ...@@ -69,8 +69,8 @@ class PDBFile(object):
Parameters Parameters
---------- ----------
file : string file : string or file
the name of the file to load the name of the file to load. Alternatively you can pass an open file object.
extraParticleIdentifier : string='EP' extraParticleIdentifier : string='EP'
if this value appears in the element column for an ATOM record, the Atom's element will be set to None to mark it as an extra particle if this value appears in the element column for an ATOM record, the Atom's element will be set to None to mark it as an extra particle
""" """
...@@ -352,9 +352,11 @@ class PDBFile(object): ...@@ -352,9 +352,11 @@ class PDBFile(object):
resName = res.name resName = res.name
if keepIds and len(res.id) < 5: if keepIds and len(res.id) < 5:
resId = res.id resId = res.id
resIC = res.insertionCode
else: else:
resId = "%4d" % ((resIndex+1)%10000) resId = "%4d" % ((resIndex+1)%10000)
if len(res.insertionCode) == 1:
resIC = res.insertionCode
else:
resIC = " " resIC = " "
if res.name in nonHeterogens: if res.name in nonHeterogens:
recordName = "ATOM " recordName = "ATOM "
......
wrappers/python/simtk/openmm/app/pdbxfile.py
View file @ 8dd60914
...@@ -397,7 +397,7 @@ class PDBxFile(object): ...@@ -397,7 +397,7 @@ class PDBxFile(object):
for (resIndex, res) in enumerate(residues): for (resIndex, res) in enumerate(residues):
if keepIds: if keepIds:
resId = res.id resId = res.id
resIC = (res.insertionCode if len(res.insertionCode) > 0 else '.') resIC = (res.insertionCode if res.insertionCode.strip() else '.')
else: else:
resId = resIndex + 1 resId = resIndex + 1
resIC = '.' resIC = '.'
......
wrappers/python/simtk/openmm/app/simulatedtempering.py 0 → 100644
View file @ 8dd60914
from __future__ import print_function
"""
simulatedtempering.py: Implements simulated tempering
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2015 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
__author__ = "Peter Eastman"
__version__ = "1.0"
import simtk.unit as unit
import math
import random
from sys import stdout
try:
import bz2
have_bz2 = True
except: have_bz2 = False
try:
import gzip
have_gzip = True
except: have_gzip = False
try:
import numpy
have_numpy = True
except: have_numpy = False
class SimulatedTempering(object):
"""SimulatedTempering implements the simulated tempering algorithm for accelerated sampling.
It runs a simulation while allowing the temperature to vary. At high temperatures, it can more easily cross
energy barriers to explore a wider area of conformation space. At low temperatures, it can thoroughly
explore each local region. For details, see Marinari, E. and Parisi, G., Europhys. Lett. 19(6). pp. 451-458 (1992).
The set of temperatures to sample can be specified in two ways. First, you can explicitly provide a list
of temperatures by using the "temperatures" argument. Alternatively, you can specify the minimum and
maximum temperatures, and the total number of temperatures to use. The temperatures are chosen spaced
exponentially between the two extremes. For example,
st = SimulatedTempering(simulation, numTemperatures=15, minTemperature=300*kelvin, maxTemperature=450*kelvin)
After creating the SimulatedTempering object, call step() on it to run the simulation.
Transitions between temperatures are performed at regular intervals, as specified by the "tempChangeInterval"
argument. For each transition, a new temperature is selected using the independence sampling method, as
described in Chodera, J. and Shirts, M., J. Chem. Phys. 135, 194110 (2011).
Simulated tempering requires a "weight factor" for each temperature. Ideally, these should be chosen so
the simulation spends equal time at every temperature. You can specify the list of weights to use with the
optional "weights" argument. If this is omitted, weights are selected automatically using the Wang-Landau
algorithm as described in Wang, F. and Landau, D. P., Phys. Rev. Lett. 86(10), pp. 2050-2053 (2001).
To properly analyze the results of the simulation, it is important to know the temperature and weight factors
at every point in time. The SimulatedTempering object functions as a reporter, writing this information
to a file or stdout at regular intervals (which should match the interval at which you save frames from the
simulation). You can specify the output file and reporting interval with the "reportFile" and "reportInterval"
arguments.
"""
def __init__(self, simulation, temperatures=None, numTemperatures=None, minTemperature=None, maxTemperature=None, weights=None, tempChangeInterval=25, reportInterval=1000, reportFile=stdout):
"""Create a new SimulatedTempering.
Parameters
----------
simulation: Simulation
The Simulation defining the System, Context, and Integrator to use
temperatures: list
The list of temperatures to use for tempering, in increasing order
numTemperatures: int
The number of temperatures to use for tempering. If temperatures is not None, this is ignored.
minTemperature: temperature
The minimum temperature to use for tempering. If temperatures is not None, this is ignored.
maxTemperature: temperature
The maximum temperature to use for tempering. If temperatures is not None, this is ignored.
weights: list
The weight factor for each temperature. If none, weights are selected automatically.
tempChangeInterval: int
The interval (in time steps) at which to attempt transitions between temperatures
reportInterval: int
The interval (in time steps) at which to write information to the report file
reportFile: string or file
The file to write reporting information to, specified as a file name or file object
"""
self.simulation = simulation
if temperatures is None:
if unit.is_quantity(minTemperature):
minTemperature = minTemperature.value_in_unit(unit.kelvin)
if unit.is_quantity(maxTemperature):
maxTemperature = maxTemperature.value_in_unit(unit.kelvin)
self.temperatures = [minTemperature*((float(maxTemperature)/minTemperature)**(i/float(numTemperatures-1))) for i in range(numTemperatures)]*unit.kelvin
else:
numTemperatures = len(temperatures)
self.temperatures = [(t.value_in_unit(unit.kelvin) if unit.is_quantity(t) else t)*unit.kelvin for t in temperatures]
if any(self.temperatures[i] >= self.temperatures[i+1] for i in range(numTemperatures-1)):
raise ValueError('The temperatures must be in strictly increasing order')
self.tempChangeInterval = tempChangeInterval
self.reportInterval = reportInterval
self.inverseTemperatures = [1.0/(unit.MOLAR_GAS_CONSTANT_R*t) for t in self.temperatures]
# If necessary, open the file we will write reports to.
self._openedFile = isinstance(reportFile, str)
if self._openedFile:
# Detect the desired compression scheme from the filename extension
# and open all files unbuffered
if reportFile.endswith('.gz'):
if not have_gzip:
raise RuntimeError("Cannot write .gz file because Python could not import gzip library")
self._out = gzip.GzipFile(fileobj=open(reportFile, 'wb', 0))
elif reportFile.endswith('.bz2'):
if not have_bz2:
raise RuntimeError("Cannot write .bz2 file because Python could not import bz2 library")
self._out = bz2.BZ2File(reportFile, 'w', 0)
else:
self._out = open(reportFile, 'w', 1)
else:
self._out = reportFile
# Initialize the weights.
if weights is None:
self._weights = [0.0]*numTemperatures
self._updateWeights = True
self._weightUpdateFactor = 1.0
self._histogram = [0]*numTemperatures
self._hasMadeTransition = False
else:
self._weights = weights
self._updateWeights = False
# Select the initial temperature.
self.currentTemperature = 0
self.simulation.integrator.setTemperature(self.temperatures[self.currentTemperature])
# Add a reporter to the simulation which will handle the updates and reports.
class STReporter(object):
def __init__(self, st):
self.st = st
def describeNextReport(self, simulation):
st = self.st
steps1 = st.tempChangeInterval - simulation.currentStep%st.tempChangeInterval
steps2 = st.reportInterval - simulation.currentStep%st.reportInterval
steps = min(steps1, steps2)
isUpdateAttempt = (steps1 == steps)
return (steps, False, isUpdateAttempt, False, isUpdateAttempt)
def report(self, simulation, state):
st = self.st
if simulation.currentStep%st.tempChangeInterval == 0:
st._attemptTemperatureChange(state)
if simulation.currentStep%st.reportInterval == 0:
st._writeReport()
simulation.reporters.append(STReporter(self))
# Write out the header line.
headers = ['Steps', 'Temperature (K)']
for t in self.temperatures:
headers.append('%gK Weight' % t.value_in_unit(unit.kelvin))
print('#"%s"' % ('"\t"').join(headers), file=self._out)
def __del__(self):
if self._openedFile:
self._out.close()
@property
def weights(self):
return [x-self._weights[0] for x in self._weights]
def step(self, steps):
"""Advance the simulation by integrating a specified number of time steps."""
self.simulation.step(steps)
def _attemptTemperatureChange(self, state):
"""Attempt to move to a different temperature."""
# Compute the probability for each temperature. This is done in log space to avoid overflow.
logProbability = [(self._weights[i]-self.inverseTemperatures[i]*state.getPotentialEnergy()) for i in range(len(self._weights))]
maxLogProb = max(logProbability)
offset = maxLogProb + math.log(sum(math.exp(x-maxLogProb) for x in logProbability))
probability = [math.exp(x-offset) for x in logProbability]
r = random.random()
for j in range(len(probability)):
if r < probability[j]:
if j != self.currentTemperature:
# Rescale the velocities.
scale = math.sqrt(self.temperatures[j]/self.temperatures[self.currentTemperature])
if have_numpy:
velocities = scale*state.getVelocities(asNumpy=True).value_in_unit(unit.nanometers/unit.picoseconds)
else:
velocities = [v*scale for v in state.getVelocities().value_in_unit(unit.nanometers/unit.picoseconds)]
self.simulation.context.setVelocities(velocities)
# Select this temperature.
self._hasMadeTransition = True
self.currentTemperature = j
self.simulation.integrator.setTemperature(self.temperatures[j])
if self._updateWeights:
# Update the weight factors.
self._weights[j] -= self._weightUpdateFactor
self._histogram[j] += 1
minCounts = min(self._histogram)
if minCounts > 20 and minCounts >= 0.2*sum(self._histogram)/len(self._histogram):
# Reduce the weight update factor and reset the histogram.
self._weightUpdateFactor *= 0.5
self._histogram = [0]*len(self.temperatures)
self._weights = [x-self._weights[0] for x in self._weights]
elif not self._hasMadeTransition and probability[self.currentTemperature] > 0.99:
# Rapidly increase the weight update factor at the start of the simulation to find
# a reasonable starting value.
self._weightUpdateFactor *= 2.0
self._histogram = [0]*len(self.temperatures)
return
r -= probability[j]
def _writeReport(self):
"""Write out a line to the report."""
temperature = self.temperatures[self.currentTemperature].value_in_unit(unit.kelvin)
values = [temperature]+self.weights
print(('%d\t' % self.simulation.currentStep) + '\t'.join('%g' % v for v in values), file=self._out)
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