def useTIP3P(self):
"""Change the appropriate lines in the topology file to use ffamber_tip3p."""
print '>> Using TIP3P water <<'
top = TopologyFile(topfile=self.files.topfile)
# print '>>> top.includes:', top.includes
# print '>>> top.ifdefs:', top.ifdefs
# Remove other water models
i = 0
TIP3PLine = False
while i < len(top.includes):
if top.includes[i].count('"ffamber_tip3p.itp"') > 0:
TIP3PLine = True
if top.includes[i].count('"spc.itp"') > 0:
print '>>> REMOVING include:', top.includes.pop(i) # remove any instances of '#include "spc.itp"'
elif top.includes[i].count('"flexspc.itp"') > 0:
print '>>> REMOVING include:', top.includes.pop(i) # remove any instances of '#include "flexspc.itp"'
else:
i += 1
# Remove any "spc.itp" mention from ifdefs too
#
# Recall that top.ifdefs are lists of ifdef groups of lines
# Example:
# [ ['#ifdef POSRES\n', '#include "posre.itp"\n', '#endif\n'],
# ['#ifdef FLEX_SPC\n', '#include "flexspc.itp"\n', '#else\n', '#include "spc.itp"\n', '#endif\n'], .... ]
i = 0
while i < len(top.ifdefs):
spcMentioned = False
for line in top.ifdefs[i]:
if line.count('spc.itp') > 0:
spcMentioned = True
break
if spcMentioned:
top.ifdefs.pop(i)
else:
i += 1
# If there's no line for ffamber_tip3p.itp, add it
if not TIP3PLine:
top.includes.append('#include "ffamber_tip3p.itp"\n')
# write the new topfile
top.rebuild_lines() # This must be done if there are any changes made the the data
top.write(self.files.next_top())
self.files.increment_top()
def extractNumberSolventMoleculesFromTopology(intopfile):
"""Extract the number of water molecules from a topology file."""
top = TopologyFile(topfile=intopfile)
# print top.nmols
try:
numberWaterMolecules = top.nmols['SOL']
except:
raise TopologyFileFormatError
return int(numberWaterMolecules)
def useTIP3P(self):
"""Change the appropriate lines in the topology file to use ffamber_tip3p."""
print '>> Using TIP3P water <<'
top = TopologyFile(topfile=self.files.topfile)
# print '>>> top.includes:', top.includes
# print '>>> top.ifdefs:', top.ifdefs
# Remove other water models
i = 0
TIP3PLine = False
while i < len(top.includes):
if top.includes[i].count('"ffamber_tip3p.itp"') > 0:
TIP3PLine = True
if top.includes[i].count('"spc.itp"') > 0:
print '>>> REMOVING include:', top.includes.pop(
i) # remove any instances of '#include "spc.itp"'
elif top.includes[i].count('"flexspc.itp"') > 0:
print '>>> REMOVING include:', top.includes.pop(
i) # remove any instances of '#include "flexspc.itp"'
else:
i += 1
# Remove any "spc.itp" mention from ifdefs too
#
# Recall that top.ifdefs are lists of ifdef groups of lines
# Example:
# [ ['#ifdef POSRES\n', '#include "posre.itp"\n', '#endif\n'],
# ['#ifdef FLEX_SPC\n', '#include "flexspc.itp"\n', '#else\n', '#include "spc.itp"\n', '#endif\n'], .... ]
i = 0
while i < len(top.ifdefs):
spcMentioned = False
for line in top.ifdefs[i]:
if line.count('spc.itp') > 0:
spcMentioned = True
break
if spcMentioned:
top.ifdefs.pop(i)
else:
i += 1
# If there's no line for ffamber_tip3p.itp, add it
if not TIP3PLine:
top.includes.append('#include "ffamber_tip3p.itp"\n')
# write the new topfile
top.rebuild_lines(
) # This must be done if there are any changes made the the data
top.write(self.files.next_top())
self.files.increment_top()
def AddIons(self, np, nn, nwaters):
"""Use the gromacs program genbox to replace water molecules in the current simulation box
with ions.
REQUIRED
np - the number of positive ions species
nn - the number of negative ions species
nwaters - the number of water molecules *currently* in the box
After the ions are added (and the water molecules replaced), there should be:
np cations, nn anions, and (nwaters-nn-np) water molecules.
"""
# If we're using the 3.1.4 version of gromacs, we first need to find the index of the solvent group
# that genbox will use to add the ions.
if self.system.gmx_version == '3.1.4':
# Get the solvent group index
solventGroupIndex = self.getSolventGroupIndexFromGenion()
# Make a new grofile with the added ions
genion = 'echo %d | %s/genion -s %s -o %s -pname %s -np %d -pq %d -nname %s -nn %d -nq %d -g genion.log -n %s ' % (
solventGroupIndex, os.environ['GMXPATH'], self.files.tprfile,
self.files.next_gro(), self.system.positiveIonName, np,
self.system.positiveIonCharge, self.system.negativeIonName, nn,
self.system.negativeIonCharge, self.files.ndxfile)
self.rungmx(genion)
self.files.increment_gro(
) # must increment filename for any new gmx file
elif self.system.gmx_version == '3.3':
# make a new grofile with the added ions
genion = '%s/genion -s %s -o %s -pname %s -np %d -pq %d -nname %s -nn %d -nq %d -g genion.log' % (
os.environ['GMXPATH'], self.files.tprfile,
self.files.next_gro(), self.system.positiveIonName, np,
self.system.positiveIonCharge, self.system.negativeIonName, nn,
self.system.negativeIonCharge)
self.rungmx(genion)
if (
np + nn
) > 0: # genion 3.3 WILL NOT produce a new gro if there is nothing to be done
self.files.increment_gro(
) # must increment filename for any new gmx file
# Generate a new index file for the ion-ated grofile
self.makeIndexFile(self.files.grofile, self.files.next_ndx())
self.files.increment_ndx(
) # must increment filename for any new gmx file
# Generate a new topology file that we will add ions to (and decrease the number of water molecules)
top = TopologyFile(topfile=self.files.topfile)
# Add ions to topology file, which will eventually be in blocks that look like so:
# [ moleculetype ]
# ; molname nrexcl
# K 1
#
# [ atoms ]
# ; id at-type res-nr residuename at-name cgnr charge mass
# 1 K 1 K K 1 1 39.098
ions = IonEnvironmentCalculation(self.system).getIons(
) # a list of Ion() objects we will use to build ion molecules
# Formatting needed for TopologyFileMolecule lines
blockText = """[ moleculetype ]
; molname nrexcl
%(molname)s 1
[ atoms ]
; id atomtype resnum residuename atoname cgnr charge mass
1 %(atom_type)s 1 %(molname)s %(molname)s 1 %(charge)d %(mass)f """
# Make a TopologyMolecule object for the negative ion
negIonDict = {}
negIonDict['molname'] = self.system.negativeIonName
negIonDict['atom_type'] = ions[self.system.negativeIonName].atomType
negIonDict['charge'] = ions[self.system.negativeIonName].charge
negIonDict['mass'] = ions[self.system.negativeIonName].atomicMass
print 'negIonDict', negIonDict
lines = [s + '\n' for s in ((blockText % negIonDict).split('\n'))]
print 'lines', lines
lines = (blockText % negIonDict).split('\n')
#lines = [(s+'\n') for s in ((blockText%negIonDict).split('\n')) ]
print 'lines', lines
negIonMolecule = TopologyFileMolecule(lines)
# Make a TopologyMolecule object for the positive ion
posIonDict = {}
posIonDict['molname'] = self.system.positiveIonName
posIonDict['atom_type'] = ions[self.system.positiveIonName].atomType
posIonDict['charge'] = ions[self.system.positiveIonName].charge
posIonDict['mass'] = ions[self.system.positiveIonName].atomicMass
lines = (blockText % posIonDict).split('\n')
# lines = [(s+'\n') for s in () ]
print 'lines', lines
posIonMolecule = TopologyFileMolecule(lines)
# Add the ion molecules to the topology file
top.AddMolecule(
negIonMolecule,
nn) # arguments: opologyFileMolecule object, NumberOfMolecules
top.AddMolecule(posIonMolecule, np)
# The number of water molecules needs to be changed to reflect the current count
numberWatersAfterGenion = nwaters - nn - np
top.nmols['SOL'] = str(numberWatersAfterGenion)
# Rebuild all the lines in the topfile and save it
top.rebuild_lines()
top.write(self.files.next_top())
self.files.increment_top(
) # PrepWorker must increment filename for any new gmx file
def AddIons(self, np, nn, nwaters):
"""Use the gromacs program genbox to replace water molecules in the current simulation box
with ions.
REQUIRED
np - the number of positive ions species
nn - the number of negative ions species
nwaters - the number of water molecules *currently* in the box
After the ions are added (and the water molecules replaced), there should be:
np cations, nn anions, and (nwaters-nn-np) water molecules.
"""
# If we're using the 3.1.4 version of gromacs, we first need to find the index of the solvent group
# that genbox will use to add the ions.
if self.system.gmx_version == '3.1.4':
# Get the solvent group index
solventGroupIndex = self.getSolventGroupIndexFromGenion()
# Make a new grofile with the added ions
genion = 'echo %d | %s/genion -s %s -o %s -pname %s -np %d -pq %d -nname %s -nn %d -nq %d -g genion.log -n %s '%(solventGroupIndex, os.environ['GMXPATH'], self.files.tprfile, self.files.next_gro(), self.system.positiveIonName, np, self.system.positiveIonCharge, self.system.negativeIonName, nn, self.system.negativeIonCharge, self.files.ndxfile)
self.rungmx( genion )
self.files.increment_gro() # must increment filename for any new gmx file
elif self.system.gmx_version == '3.3':
# make a new grofile with the added ions
genion = '%s/genion -s %s -o %s -pname %s -np %d -pq %d -nname %s -nn %d -nq %d -g genion.log'%(os.environ['GMXPATH'], self.files.tprfile, self.files.next_gro(), self.system.positiveIonName, np, self.system.positiveIonCharge, self.system.negativeIonName, nn, self.system.negativeIonCharge)
self.rungmx( genion )
if (np+nn) > 0: # genion 3.3 WILL NOT produce a new gro if there is nothing to be done
self.files.increment_gro() # must increment filename for any new gmx file
# Generate a new index file for the ion-ated grofile
self.makeIndexFile(self.files.grofile, self.files.next_ndx())
self.files.increment_ndx() # must increment filename for any new gmx file
# Generate a new topology file that we will add ions to (and decrease the number of water molecules)
top = TopologyFile(topfile=self.files.topfile)
# Add ions to topology file, which will eventually be in blocks that look like so:
# [ moleculetype ]
# ; molname nrexcl
# K 1
#
# [ atoms ]
# ; id at-type res-nr residuename at-name cgnr charge mass
# 1 K 1 K K 1 1 39.098
ions = IonEnvironmentCalculation(self.system).getIons() # a list of Ion() objects we will use to build ion molecules
# Formatting needed for TopologyFileMolecule lines
blockText = """[ moleculetype ]
; molname nrexcl
%(molname)s 1
[ atoms ]
; id atomtype resnum residuename atoname cgnr charge mass
1 %(atom_type)s 1 %(molname)s %(molname)s 1 %(charge)d %(mass)f """
# Make a TopologyMolecule object for the negative ion
negIonDict = {}
negIonDict['molname'] = self.system.negativeIonName
negIonDict['atom_type'] = ions[self.system.negativeIonName].atomType
negIonDict['charge'] = ions[self.system.negativeIonName].charge
negIonDict['mass'] = ions[self.system.negativeIonName].atomicMass
print 'negIonDict', negIonDict
lines = [s+'\n' for s in ((blockText%negIonDict).split('\n')) ]
print 'lines', lines
lines = (blockText%negIonDict).split('\n')
#lines = [(s+'\n') for s in ((blockText%negIonDict).split('\n')) ]
print 'lines', lines
negIonMolecule = TopologyFileMolecule( lines )
# Make a TopologyMolecule object for the positive ion
posIonDict = {}
posIonDict['molname'] = self.system.positiveIonName
posIonDict['atom_type'] = ions[self.system.positiveIonName].atomType
posIonDict['charge'] = ions[self.system.positiveIonName].charge
posIonDict['mass'] = ions[self.system.positiveIonName].atomicMass
lines = (blockText%posIonDict).split('\n')
# lines = [(s+'\n') for s in () ]
print 'lines', lines
posIonMolecule = TopologyFileMolecule( lines )
# Add the ion molecules to the topology file
top.AddMolecule(negIonMolecule, nn) # arguments: opologyFileMolecule object, NumberOfMolecules
top.AddMolecule(posIonMolecule, np)
# The number of water molecules needs to be changed to reflect the current count
numberWatersAfterGenion = nwaters-nn-np
top.nmols['SOL'] = str(numberWatersAfterGenion)
# Rebuild all the lines in the topfile and save it
top.rebuild_lines()
top.write(self.files.next_top())
self.files.increment_top() # PrepWorker must increment filename for any new gmx file