props = ['id', 'pos', 'v', 'type', 'mass', 'q']
allParticles = []
for pid in range(num_particles):
part = [
pid + 1,
Real3D(x[pid], y[pid], z[pid]),
Real3D(vx[pid], vy[pid], vz[pid]), types[pid], masses[pid],
charges[pid]
]
allParticles.append(part)
system.storage.addParticles(allParticles, *props)
system.storage.decompose()
# set up LJ interaction according to the parameters read from the .top file
ljinteraction = gromacs.setLennardJonesInteractions(system, defaults,
atomtypeparameters,
verletlist, rc)
# set up angle interactions according to the parameters read from the .top file
angleinteractions = gromacs.setAngleInteractions(system, angletypes,
angletypeparams)
# set up coulomb interactions according to the parameters read from the .top file
# !! Warning: this only works for reaction-field now!
qq_interactions = gromacs.setCoulombInteractions(system,
verletlist,
rc,
types,
epsilon1=1,
epsilon2=80,
kappa=0)
print "#No thermostat"
########################################################################
# 6. define atomistic and adres interactions
########################################################################
## adres interactions ##
print '# moving atomistic region composed of multiple spheres centered on each protein cg particle'
particlePIDsADR = [mapAtToCgIndex[pid] for pid in particlePIDsADR]
verletlist = espressopp.VerletListAdress(system, cutoff=nbCutoff, adrcut=nbCutoff,
dEx=ex_size, dHy=hy_size,
pids=particlePIDsADR, sphereAdr=True)
# set up LJ interaction according to the parameters read from the .top file
lj_adres_interaction=gromacs.setLennardJonesInteractions(system, defaults, atomtypeparameters, verletlist, intCutoff, adress=True, ftpl=ftpl)
# set up coulomb interactions according to the parameters read from the .top file
print '#Note: Reaction Field method is used for Coulomb interactions'
qq_adres_interaction=gromacs.setCoulombInteractions(system, verletlist, intCutoff, atTypes, epsilon1=1, epsilon2=67.5998, kappa=0, adress=True, ftpl=ftpl)
# set the CG potential for water. Set for LJ interaction, and QQ interaction has no CG equivalent, also prot has no CG potential, is always in adres region
# load CG interaction from table
fe="table_CGwat_CGwat.tab"
gromacs.convertTable("table_CGwat_CGwat.xvg", fe, 1, 1, 1, 1)
potCG = espressopp.interaction.Tabulated(itype=3, filename=fe, cutoff=intCutoff)
lj_adres_interaction.setPotentialCG(type1=typeCG, type2=typeCG, potential=potCG)
## bonded (fixed list) interactions for protein (actually between CG particles in AA region) ##
## set up LJ 1-4 interactions
print "Adding particles to storage..."
system.storage.addParticles(allParticles, *props)
# create FixedTupleList object and add the tuples
print "Building FixedTupleListAdress..."
ftpl = espressopp.FixedTupleListAdress(system.storage)
ftpl.addTuples(tuples)
system.storage.setFixedTuplesAdress(ftpl)
system.storage.decompose()
print "Set up interactions..."
# set up LJ interaction according to the parameters read from the .top file
ljinteraction = gromacs.setLennardJonesInteractions(system,
defaults,
atomtypeparameters,
verletlist,
rca,
hadress=True,
ftpl=ftpl)
# set up angle interactions according to the parameters read from the .top file
# COMMMENTED OUT BECAUSE OF SETTLE
#fpl = espressopp.FixedTripleListAdress(system.storage, ftpl)
#angleinteractions=gromacs.setAngleInteractions(system, angletypes, angletypeparams,fpl)
#fpl = espressopp.FixedTripleListAdress(system.storage, ftpl)
# set up coulomb interactions according to the parameters read from the .top file
# !! Warning: this only works for reaction-field now!
qq_interactions = gromacs.setCoulombInteractions(system,
verletlist,
rca,
# append tuple to tuplelist
tuples.append(tmptuple)
system.storage.addParticles(allParticles, *props)
# create FixedTupleList object
ftpl = espressopp.FixedTupleListAdress(system.storage)
# and add the tuples
ftpl.addTuples(tuples)
system.storage.setFixedTuplesAdress(ftpl)
system.storage.decompose()
# set up LJ interaction according to the parameters read from the .top file
ljinteraction=gromacs.setLennardJonesInteractions(system, defaults, atomtypeparameters, verletlist,rca, hadress=True, ftpl=ftpl)
# set up angle interactions according to the parameters read from the .top file
#fpl = espressopp.FixedTripleListAdress(system.storage, ftpl)
angleinteractions=gromacs.setAngleInteractionsAdress(system, angletypes, angletypeparams, ftpl)
# set up coulomb interactions according to the parameters read from the .top file
# !! Warning: this only works for reaction-field now!
qq_interactions=gromacs.setCoulombInteractions(system, verletlist, rca, types, epsilon1=1, epsilon2=80, kappa=0, hadress=True, ftpl=ftpl)
# load CG interaction from table
fe="table_CG_CG.tab"
gromacs.convertTable("table_CG_CG.xvg", fe, 1, 1, 1, 1)
potCG = espressopp.interaction.Tabulated(itype=3, filename=fe, cutoff=rca) # CG
allParticles = []
for pid in range(num_particles):
part = [
pid + 1,
Real3D(x[pid], y[pid], z[pid]),
Real3D(vx[pid], vy[pid], vz[pid]),
types[pid],
masses[pid],
charges[pid],
]
allParticles.append(part)
system.storage.addParticles(allParticles, *props)
system.storage.decompose()
# set up LJ interaction according to the parameters read from the .top file
ljinteraction = gromacs.setLennardJonesInteractions(system, defaults, atomtypeparameters, verletlist, rc)
# set up angle interactions according to the parameters read from the .top file
angleinteractions = gromacs.setAngleInteractions(system, angletypes, angletypeparams)
# set up coulomb interactions according to the parameters read from the .top file
# !! Warning: this only works for reaction-field now!
qq_interactions = gromacs.setCoulombInteractions(system, verletlist, rc, types, epsilon1=1, epsilon2=80, kappa=0)
# set up bonded interactions according to the parameters read from the .top file
bondedinteractions = gromacs.setBondedInteractions(system, bondtypes, bondtypeparams)
# exlusions, i.e. pairs of atoms not considered for the non-bonded part. Those are defined either by bonds which automatically generate an exclusion. Or by the nregxcl variable
verletlist.exclude(exclusions)
# langevin thermostat
