print "# nbCutoff = ", nbCutoff
print "# intCutoff = ", intCutoff
print "# skin = ", skin
print "# dt = ", dt
print "# nSteps = ", nSteps
print "# output every ", nStepsPerOutput, " steps"
########################################################################
# 2. read in coordinates and topology
########################################################################
## get info on (complete) atomistic system ##
print '# Reading gromacs top and gro files...'
# call gromacs parser for processing the top file (and included files) and the gro file
defaults, atTypes, atomtypesDict, atMasses, atCharges, atomtypeparameters, atBondtypes, bondtypeparams, atAngletypes, angletypeparams, atDihedraltypes, dihedraltypeparams, atImpropertypes, impropertypeparams, atExclusions, atOnefourpairslist, atX, atY, atZ, atVX, atVY, atVZ, atResnames, atResid, Lx, Ly, Lz = gromacs.read(
inputcrdfile, aatopfile)
#initialize a map between atomtypes as integers and as strings
reverseAtomtypesDict = dict([(v, k) for k, v in atomtypesDict.iteritems()])
# delete from atomtypeparams any types not in system, so as not to conflict with any new types created later
for k in list(atomtypeparameters):
if k not in atTypes:
print "# Deleting unused type ", k, "/", reverseAtomtypesDict[
k], " from atomtypeparameters, atomtypesDict and reverseAtomtypesDict"
del atomtypeparameters[k]
atomtypekey = reverseAtomtypesDict[k]
del reverseAtomtypesDict[k]
del atomtypesDict[atomtypekey]
# system box size
box = (Lx, Ly, Lz)
skin = 0.03
timestep = 0.0005
# parameters to convert GROMACS tabulated potential file
sigma = 1.0
epsilon = 1.0
c6 = 1.0
c12 = 1.0
# GROMACS setup files
grofile = "conf.gro"
topfile = "topol.top"
# this calls the gromacs parser for processing the top file (and included files) and the conf file
# The variables at the beginning defaults, types, etc... can be found by calling
# gromacs.read(grofile,topfile) without return values. It then prints out the variables to be unpacked
defaults, types, atomtypes, masses, charges, atomtypeparameters, bondtypes, bondtypeparams, angletypes, angletypeparams, exclusions, x, y, z, vx, vy, vz, resname, resid, Lx, Ly, Lz = gromacs.read(
grofile, topfile)
######################################################################
## IT SHOULD BE UNNECESSARY TO MAKE MODIFICATIONS BELOW THIS LINE ##
######################################################################
#types, bonds, angles, dihedrals, x, y, z, vx, vy, vz, Lx, Ly, Lz = gromacs.read(grofile,topfile)
#defaults, types, masses, charges, atomtypeparameters, bondtypes, bondtypeparams, angletypes, angletypeparams, exclusions, x, y, z, vx, vy, vz, Lx, Ly, Lz = gromacs.read(grofile,topfile)
num_particles = len(x)
density = num_particles / (Lx * Ly * Lz)
size = (Lx, Ly, Lz)
print size
sys.stdout.write('Setting up simulation ...\n')
system = espressopp.System()
system.rng = espressopp.esutil.RNG()
