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 '# 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)
# append tuple to tuplelist
tuples.append(tmptuple)
system.storage.addParticles(allParticles, *props)
# create FixedTupleList object and add the tuples
ftpl = espressopp.FixedTupleListAdress(system.storage)
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
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,