def make_system(molecules,
numbers,
ff,
box=None,
virtual_sites=False,
drudes=False):
from shutil import which
from mstools.wrapper import Packmol
packmol_path = which("packmol")
packmol = Packmol(packmol_path)
# convert to nm - nargs gives a list
if len(box) == 1:
box = [b / 10 for b in box] * 3
else:
box = [b / 10 for b in box]
top = Topology(molecules)
top.generate_angle_dihedral_improper()
if virtual_sites:
top.generate_virtual_sites(ff)
if drudes:
top.generate_drude_particles(ff)
top.assign_charge_from_ff(ff)
top.cell.set_box(box)
top.scale_with_packmol(numbers, packmol)
return System(top, ff)
if mol.has_position:
logger.warning(f'{str(mol)} carries no bond. Guessing connectivity from FF')
mol.guess_connectivity_from_ff(ff, angle_tolerance=15, pbc='xyz', cell=top.cell)
else:
logger.warning(f'{str(mol)} carries no bond. Make sure the topology is correct')
if ff.is_polarizable:
mol.generate_drude_particles(ff)
if ff.has_virtual_site:
mol.generate_virtual_sites(ff)
mol.assign_mass_from_ff(ff)
mol.assign_charge_from_ff(ff)
if args.packmol:
top.update_molecules(list(mol_count.keys()))
top.scale_with_packmol(list(mol_count.values()))
sys.exit(0)
logger.info('Exporting ...')
top.update_molecules(list(mol_count.keys()), list(mol_count.values()))
if args.trj is None:
logger.warning('Trajectory file not provided. '
'Will use positions and cell from the topology')
else:
_positions_set = False
if len(frame.positions) == top.n_atom:
top.set_positions(frame.positions)
_positions_set = True
elif ff.is_polarizable or ff.has_virtual_site:
h_1
c_4
c_4h2
c_4h3
'''
typer = ZftTyper(io.StringIO(definition))
butane = Molecule.from_smiles('CCCC butane')
typer.type_molecule(butane)
# Load force field parameters from ZFP file
ff = ForceField.open('alkane.zfp')
# Initialize a topology with periodic boundary condition
# For now, it contains only one butane molecule
top = Topology([butane], cell=UnitCell([3, 3, 3]))
# Assign atomic charges based on the charge parameters in the force field
top.assign_charge_from_ff(ff)
# Call Packmol to build a configuration containing 100 butane molecules
packmol = Packmol(r'/path/of/packmol')
top.scale_with_packmol([100], packmol=packmol)
# Associate force field parameters to the topology
# And then export input files for simulation engines
system = System(top, ff)
system.export_gromacs()
system.export_lammps()
system.export_charmm()
