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
langevin = espresso.integrator.LangevinThermostat(system)
langevin.gamma = 2.0
langevin.temperature = 2.4942 # kT in gromacs units
integrator = espresso.integrator.VelocityVerlet(system)
integrator.addExtension(langevin)
integrator.dt = timestep
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 = espresso.FixedTripleListAdress(system.storage, ftpl)
angleinteractions=gromacs.setAngleInteractions(system, angletypes, angletypeparams, fpl)
# 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 = espresso.interaction.Tabulated(itype=3, filename=fe, cutoff=rca) # CG
# set the CG potential. There are two non-bonded interactions, we pick only the first one
for n in range(system.getNumberOfInteractions()):
interaction=system.getInteraction(n)
if interaction.bondType() == espresso.interaction.Nonbonded:
print "Setting CG interaction", typeCG
interaction.setPotentialCG(type1=typeCG, type2=typeCG, potential=potCG)
break
