def createSystem(self,
nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=1.0 * nanometer,
ewaldErrorTolerance=0.0005,
removeCMMotion=True,
hydrogenMass=None,
OPLS=False,
implicitSolvent=None,
AGBNPVersion=1):
"""Construct an OpenMM System representing the topology described by this
DMS file
Parameters
----------
nonbondedMethod : object=NoCutoff
The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
nonbondedCutoff : distance=1*nanometer
The cutoff distance to use for nonbonded interactions
ewaldErrorTolerance : float=0.0005
The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
removeCMMotion : boolean=True
If true, a CMMotionRemover will be added to the System
hydrogenMass : mass=None
The mass to use for hydrogen atoms bound to heavy atoms. Any mass
added to a hydrogen is subtracted from the heavy atom to keep their
total mass the same.
OPLS : boolean=False
If True, forces OPLS combining rules
implicitSolvent: string=None
If not None, creates implicit solvent force of the given name
Allowed values are: HCT and 'AGBNP'
(the corresponding tables must be present in the DMS file)
AGBNPVersion: int=1
AGBNP implicit solvent version
"""
self._checkForUnsupportedTerms()
sys = mm.System()
# Build the box dimensions
boxSize = self.topology.getUnitCellDimensions()
if boxSize is not None:
sys.setDefaultPeriodicBoxVectors(
(boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2]))
elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME,
ff.LJPME):
raise ValueError(
'Illegal nonbonded method for a non-periodic system')
# Create all of the particles
for (fcounter, conn, tables, offset) in self._localVars():
for mass in conn.execute('SELECT mass FROM particle ORDER BY id'):
sys.addParticle(mass[0] * dalton)
# Add all of the forces
self._addBondsToSystem(sys)
self._addAnglesToSystem(sys)
self._addConstraintsToSystem(sys)
self._addPeriodicTorsionsToSystem(sys, OPLS)
self._addImproperHarmonicTorsionsToSystem(sys)
self._addCMAPToSystem(sys)
self._addVirtualSitesToSystem(sys)
self._addPositionalHarmonicRestraints(sys)
nb, cnb = self._addNonbondedForceToSystem(sys, OPLS)
# Finish configuring the NonbondedForce.
methodMap = {
ff.NoCutoff: mm.NonbondedForce.NoCutoff,
ff.CutoffNonPeriodic: mm.NonbondedForce.CutoffNonPeriodic,
ff.CutoffPeriodic: mm.NonbondedForce.CutoffPeriodic,
ff.Ewald: mm.NonbondedForce.Ewald,
ff.PME: mm.NonbondedForce.PME,
ff.LJPME: mm.NonbondedForce.LJPME
}
nb.setNonbondedMethod(methodMap[nonbondedMethod])
nb.setCutoffDistance(nonbondedCutoff)
nb.setEwaldErrorTolerance(ewaldErrorTolerance)
if cnb is not None:
nb.setUseDispersionCorrection(False)
if nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME,
ff.LJPME):
cnb.setNonbondedMethod(methodMap[ff.CutoffPeriodic])
cnb.setCutoffDistance(nonbondedCutoff)
elif nonbondedMethod == ff.CutoffNonPeriodic:
cnb.setNonbondedMethod(methodMap[ff.CutoffNonPeriodic])
cnb.setCutoffDistance(nonbondedCutoff)
else:
cnb.setNonbondedMethod(methodMap[ff.NoCutoff])
cnb.setUseSwitchingFunction(False)
cnb.setUseLongRangeCorrection(False)
#add implicit solvent model.
if implicitSolvent is not None:
if not (implicitSolvent in (HCT, 'AGBNP', 'GVolSA', 'AGBNP3')):
raise ValueError('Illegal implicit solvent method')
if self._verbose:
print('Adding implicit solvent ...')
#with implicit solvent turn off native reaction field
#However note that this does not affect the shifted Coulomb potential of the Nonbonded force
#(it affects the only the energy, not the forces and equation of motion)
nb.setReactionFieldDielectric(1.0)
if implicitSolvent is HCT:
gb_parms = self._get_gb_params()
if gb_parms:
if self._verbose:
print('Adding HCT GB force ...')
gb = GBSAHCTForce(SA='ACE')
for i in range(len(gb_parms)):
gb.addParticle(list(gb_parms[i]))
gb.finalize()
sys.addForce(gb)
else:
raise IOError("No HCT parameters found in DMS file")
if implicitSolvent is 'AGBNP3':
#load AGBNP3 plugin if available
try:
from AGBNP3plugin import AGBNP3Force
except ImportError:
raise NotImplementedError(
'AGBNP3 is not supported in this version')
#sets up AGBNP3
gb_parms = self._get_agbnp2_params()
if gb_parms:
if self._verbose:
print('Adding AGBNP3 force ...')
gb = AGBNP3Force()
# add particles
for i in range(len(gb_parms)):
p = gb_parms[i]
gb.addParticle(p[0], p[1], p[2], p[3], p[4], p[5],
p[6])
# connection table (from bonds)
self._add_agbnp2_ct(gb)
sys.addForce(gb)
else:
raise IOError("No AGBNP parameters found in DMS file")
if implicitSolvent is 'GVolSA':
#implemented as AGBNP version 0
implicitSolvent = 'AGBNP'
AGBNPVersion = 0
if self._verbose:
print('Using GVolSA')
if implicitSolvent is 'AGBNP':
#load AGBNP plugin if available
try:
from AGBNPplugin import AGBNPForce
except ImportError:
raise NotImplementedError(
'AGBNP is not supported in this version')
#sets up AGBNP
gb_parms = self._get_agbnp2_params()
if gb_parms:
gb = AGBNPForce()
gb.setNonbondedMethod(methodMap[nonbondedMethod])
gb.setCutoffDistance(nonbondedCutoff)
gb.setVersion(AGBNPVersion)
if self._verbose:
print('Using AGBNP force version %d ...' %
AGBNPVersion)
# add particles
for i in range(len(gb_parms)):
[
radiusN, chargeN, gammaN, alphaN, hbtype, hbwN,
ishydrogenN
] = gb_parms[i]
h_flag = ishydrogenN > 0
gb.addParticle(radiusN, gammaN, alphaN, chargeN,
h_flag)
sys.addForce(gb)
self.gb_parms = gb_parms
self.agbnp = gb
else:
raise IOError("No AGBNP parameters found in DMS file")
# Adjust masses.
if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds():
if atom1.element == hydrogen:
(atom1, atom2) = (atom2, atom1)
if atom2.element == hydrogen and atom1.element not in (
hydrogen, None):
transferMass = hydrogenMass - sys.getParticleMass(
atom2.index)
sys.setParticleMass(atom2.index, hydrogenMass)
sys.setParticleMass(
atom1.index,
sys.getParticleMass(atom1.index) - transferMass)
# Add a CMMotionRemover.
if removeCMMotion:
sys.addForce(mm.CMMotionRemover())
return sys
def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*nanometer,
ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None, OPLS=False, implicitSolvent=None):
"""Construct an OpenMM System representing the topology described by this dms file
Parameters:
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
- nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
- ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
- hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is
subtracted from the heavy atom to keep their total mass the same.
- OPLS (boolean=False) If True, force field parameters are interpreted as OPLS parameters; OPLS variants of
torsional and non-bonded forces are constructed.
- implicitSolvent (object=None) if not None, the implicit solvent model to use, the only allowed value is HCT
"""
self._checkForUnsupportedTerms()
sys = mm.System()
# Buld the box dimensions
sys = mm.System()
boxSize = self.topology.getUnitCellDimensions()
if boxSize is not None:
sys.setDefaultPeriodicBoxVectors((boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2]))
elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
raise ValueError('Illegal nonbonded method for a non-periodic system')
# Create all of the particles
for mass in self._conn.execute('SELECT mass FROM particle ORDER BY id'):
sys.addParticle(mass[0]*dalton)
# Add all of the forces
self._addBondsToSystem(sys)
self._addAnglesToSystem(sys)
self._addConstraintsToSystem(sys)
self._addPeriodicTorsionsToSystem(sys, OPLS)
self._addImproperHarmonicTorsionsToSystem(sys)
self._addCMAPToSystem(sys)
self._addVirtualSitesToSystem(sys)
nb, cnb = self._addNonbondedForceToSystem(sys, OPLS)
# Finish configuring the NonbondedForce.
methodMap = {ff.NoCutoff:mm.NonbondedForce.NoCutoff,
ff.CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
ff.CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
ff.Ewald:mm.NonbondedForce.Ewald,
ff.PME:mm.NonbondedForce.PME}
nb.setNonbondedMethod(methodMap[nonbondedMethod])
nb.setCutoffDistance(nonbondedCutoff)
nb.setEwaldErrorTolerance(ewaldErrorTolerance)
if cnb is not None:
cnb.setNonbondedMethod(methodMap[nonbondedMethod])
cnb.setCutoffDistance(nonbondedCutoff)
#add implicit solvent model. Right now, only HCT model is considered.
if implicitSolvent is not None:
print('Adding implicit solvent ...')
if implicitSolvent is HCT:
gb_parms = self._get_gb_params()
if gb_parms:
print('Adding HCT GB force ...')
gb = GBSAHCTForce(SA='ACE')
for i in range(len(gb_parms)):
gb.addParticle(list(gb_parms[i]))
sys.addForce(gb)
if implicitSolvent is 'AGBNP':
#load AGBNP3 plugin if available
try:
from AGBNP3plugin import AGBNP3Force
AGBNP3enabled = True
except ImportError:
AGBNP3enabled = False
#sets up AGBNP3
if AGBNP3enabled:
gb_parms = self._get_agbnp2_params()
if gb_parms:
print('Adding AGBNP3 force ...')
gb = AGBNP3Force()
# add particles
for i in range(len(gb_parms)):
p = gb_parms[i]
gb.addParticle(p[0],p[1],p[2],p[3],p[4],p[5],p[6])
# connection table (from bonds)
self._add_agbnp2_ct(gb)
sys.addForce(gb)
else:
print('Warning: AGBNP is not supported in this version')
if implicitSolvent is 'GVolSA':
#load Gaussvol plugin if available
try:
from GVolplugin import GVolForce
GVolEnabled = True
except ImportError:
GVolEnabled = False
#sets up GVol
if GVolEnabled:
gb_parms = self._get_agbnp2_params()
if gb_parms:
print('Adding GVol force ...')
gb = GVolForce()
gb.setNonbondedMethod(methodMap[nonbondedMethod])
gb.setCutoffDistance(nonbondedCutoff)
# add particles
for i in range(len(gb_parms)):
[radiusN,chargeN,gammaN,alphaN,hbtype,hbwN,ishydrogenN] = gb_parms[i]
h_flag = ishydrogenN > 0
Roffset = 0.05;
radiusN += Roffset;
gb.addParticle(radiusN, gammaN, h_flag)
#print "Adding", radiusN, gammaN, h_flag
print "Adding GVolforce ..."
sys.addForce(gb)
print "Done"
else:
print('Warning: GVol is not supported in this version')
# Adjust masses.
if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds():
if atom1.element == hydrogen:
(atom1, atom2) = (atom2, atom1)
if atom2.element == hydrogen and atom1.element not in (hydrogen, None):
transferMass = hydrogenMass-sys.getParticleMass(atom2.index)
sys.setParticleMass(atom2.index, hydrogenMass)
sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass)
# Add a CMMotionRemover.
if removeCMMotion:
sys.addForce(mm.CMMotionRemover())
return sys
