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