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()
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)
timestep = 0.0002
# 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, 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)
num_particles = len(x)
density = num_particles / (Lx * Ly * Lz)
size = (Lx, Ly, Lz)
sys.stdout.write('Setting up simulation ...\n')
system = espressopp.System()
system.rng = espressopp.esutil.RNG()
system.bc = espressopp.bc.OrthorhombicBC(system.rng, size)
system.skin = skin
interaction_cutoff_at = 1.0 # cutoff atomistic potential
interaction_cutoff_verletlist_at = 1.25 # cutoff atomistic potential in verlet list cutoff (larger than normal atomistic interaction cutoff, since verletlist is built using CG particles)
skin = 0.05 # verlet list skin
ex_size = 2.2 # radius of atomistic region
hy_size = 1.0 # width of hybrid region
correction_on_slow_timescale = False # apply corrections on slow timescale?
######################
# 2. read in coordinates #
######################
print('Reading in coordinates... (not equilibrated!)')
# call the gromacs parser for processing the top file (and included files) and the conf file (note that this configuration is most likely not equilibrated)
defaults, types, atomtypes, masses, charges, atomtypeparameters, bondtypes, bondtypeparams, angletypes, angletypeparams, exclusions, x, y, z, vx, vy, vz, resname, resid, Lx, Ly, Lz = gromacs.read(
"conf.gro", "topol.top")
# particles, geometry, density
num_particles_AT = len(x)
num_particles_CG = len(x) // 3
density = num_particles_AT / (Lx * Ly * Lz)
size = (Lx, Ly, Lz)
#####################
# 3. set up the system #
#####################
print('Setting up system...')
# system, boundary conditions, skin, communicator, node & cell grids
system = espressopp.System()
system.bc = espressopp.bc.OrthorhombicBC(system.rng, size)
