# 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 = espressopp.integrator.LangevinThermostat(system) langevin.gamma = 10 langevin.temperature = 2.4942 # kT in gromacs units integrator = espressopp.integrator.VelocityVerlet(system) integrator.addExtension(langevin) integrator.dt = timestep print "POT", potentials pathintegral.createPathintegralSystem(allParticles, props, types, system, langevin, potentials, P=16) system.storage.decompose() num_particles = int(espressopp.analysis.NPart(system).compute()) # print simulation parameters print '' print 'number of particles =', num_particles print 'density = %.4f' % (density) print 'rc =', rc print 'dt =', integrator.dt print 'skin =', system.skin print 'steps =', steps print 'NodeGrid = %s' % (nodeGrid,) print 'CellGrid = %s' % (cellGrid,) print ''
# 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 = espressopp.integrator.LangevinThermostat(system)
langevin.gamma = 10
langevin.temperature = 2.4942 # kT in gromacs units
integrator = espressopp.integrator.VelocityVerlet(system)
integrator.addExtension(langevin)
integrator.dt = timestep
print "POT", potentials
pathintegral.createPathintegralSystem(allParticles,
props,
types,
system,
langevin,
potentials,
P=16)
system.storage.decompose()
num_particles = int(espressopp.analysis.NPart(system).compute())
# print simulation parameters
print ''
print 'number of particles =', num_particles
print 'density = %.4f' % (density)
print 'rc =', rc
print 'dt =', integrator.dt
print 'skin =', system.skin
print 'steps =', steps