hoomd.init.read_gsd(filename, restart='restart.gsd')
atomtypes = martini_hoomd.get_atom_types()
hoomd.util.quiet_status()
martini_hoomd.set_bonds()
#martini_hoomd.set_harmonic_angles(timtails = True) # For using harmonic-fit potentials
martini_hoomd.set_cosine_angles(timtails=options.timtails)
nl = hoomd.md.nlist.cell()
# Set exclusions only if using martinitim
martini_hoomd.set_exclusions(nl=nl)
if options.timtails:
table_dir = "lambda0.9-martinitim"
else:
table_dir = "lambda0.9-martinifull"
lamb0 = martini_hoomd.set_pairs(table_dir=table_dir, nl=nl)
# Define some groups
all = hoomd.group.all()
hoomd.util.unquiet_status()
# Output parameters
hoomd.analyze.log(
filename="em1.log",
quantities=['potential_energy', 'temperature', 'lx', 'ly', 'lz'],
period=500,
overwrite=True)
# If this is a continuation script, just append to the trajectory
hoomd.dump.gsd("trajectory.gsd", period=500, group=all, phase=0)
# Restart files should overwrite and replace frame 0
hoomd.dump.gsd("restart.gsd",
# load a structure, generated from mbuild
hoomd.init.read_gsd(filename, restart='restart.gsd')
#hoomd.init.read_gsd('trajectory.gsd')
atomtypes = martini_hoomd.get_atom_types()
ENERGY_TABLE, DISTANCE_TABLE, FORCE_TABLE = martini_hoomd.get_table_units()
hoomd.util.quiet_status()
martini_hoomd.set_bonds()
#martini_hoomd.set_harmonic_angles(timtails = True) # For using harmonic-fit potentials
martini_hoomd.set_cosine_angles(timtails=False)
nl = hoomd.md.nlist.cell()
# Set exclusions only if using martinitim
#martini_hoomd.set_exclusions(nl=nl)
#lamb0 = martini_hoomd.set_pairs(table_dir = "lambda0-martinitim",nl=nl)
lamb0 = martini_hoomd.set_pairs(table_dir="lambda0-martinifull", nl=nl)
# Set reaction field parameters
#martini_hoomd.set_reactionfield_electrostatics(nl=nl)
# Define some groups
all = hoomd.group.all()
hoomd.util.unquiet_status()
# Output parameters
hoomd.analyze.log(
filename="log-output.log",
quantities=['potential_energy', 'temperature', 'lx', 'ly', 'lz'],
period=100,
overwrite=True)