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