Writers

mBuild utilizes ParmEd to write Compound information to a variety of file formats (e.g. PDB, MOL2, GRO. The full list of formats supported by ParmEd can be found at http://parmed.github.io/ParmEd/html/readwrite.html). Additionally, mBuild features several internal writers for file formats not yet supported by ParmEd. Information on these internal writers can be found below.

By default, mBuild will only write coordinate and bond information to these files, i.e. no angles or dihedrals, and no atom typing is performed (atom names are used as atom types). However, force fields can be applied to Compounds by passing force field XML files (used by the Foyer package - https://github.com/mosdef-hub/foyer) to the save function if Foyer is installed. If a force field is applied to a Compound, the mBuild internal writers will also write angle and dihedral information to the file in addition to labelling atoms by the atom types specified by the force field.

GSD (General Simulation Data)

Default data file format for HOOMD v2

mbuild.formats.gsdwriter.write_gsd(structure, filename, ref_distance=1.0, ref_mass=1.0, ref_energy=1.0, rigid_bodies=None, shift_coords=True, write_special_pairs=True, **kwargs)

Output a GSD file (HOOMD v2 default data format).

Parameters:

structure : parmed.Structure

ParmEd Structure object

filename : str

Path of the output file.

ref_distance : float, optional, default=1.0

Reference distance for conversion to reduced units

ref_mass : float, optional, default=1.0

Reference mass for conversion to reduced units

ref_energy : float, optional, default=1.0

Reference energy for conversion to reduced units

rigid_bodies : list of int, optional, default=None

List of rigid body information. An integer value is required for each atom corresponding to the index of the rigid body the particle is to be associated with. A value of None indicates the atom is not part of a rigid body.

shift_coords : bool, optional, default=True

Shift coordinates from (0, L) to (-L/2, L/2) if necessary.

write_special_pairs : bool, optional, default=True

Writes out special pair information necessary to correctly use the OPLS fudged 1,4 interactions in HOOMD.

Notes

Force field parameters are not written to the GSD file and must be included manually into a HOOMD input script.

HOOMD XML

Default data file format for HOOMD v1

LAMMPS data

Default data file format for LAMMPS

mbuild.formats.lammpsdata.write_lammpsdata(structure, filename, atom_style='full', unit_style='real', detect_forcefield_style=True, nbfix_in_data_file=True, use_urey_bradleys=False, use_rb_torsions=True, use_dihedrals=False)

Output a LAMMPS data file.

Outputs a LAMMPS data file in the ‘full’ atom style format. Default units are ‘real’ units. See http://lammps.sandia.gov/doc/atom_style.html for more information on atom styles.

Parameters:

structure : parmed.Structure

ParmEd structure object

filename : str

Path of the output file

atom_style: str

Defines the style of atoms to be saved in a LAMMPS data file. The following atom styles are currently supported: ‘full’, ‘atomic’, ‘charge’, ‘molecular’ see http://lammps.sandia.gov/doc/atom_style.html for more information on atom styles.

unit_style: str

Defines to unit style to be save in a LAMMPS data file. Defaults to ‘real’ units. Current styles are supported: ‘real’, ‘lj’ see https://lammps.sandia.gov/doc/99/units.html for more information on unit styles

detect_forcefield_style: boolean

If True, format lammpsdata parameters based on the contents of the parmed Structure

use_urey_bradleys: boolean

If True, will treat angles as CHARMM-style angles with urey bradley terms while looking for structure.urey_bradleys

use_rb_torsions:

If True, will treat dihedrals OPLS-style torsions while looking for structure.rb_torsions

use_dihedrals:

If True, will treat dihedrals as CHARMM-style dihedrals while looking for structure.dihedrals

Notes

See http://lammps.sandia.gov/doc/2001/data_format.html for a full description of the LAMMPS data format. Currently the following sections are supported (in addition to the header): Masses, Nonbond Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Atoms, Bonds, Angles, Dihedrals, Impropers OPLS and CHARMM forcefield styles are supported, AMBER forcefield styles are NOT

Some of this function has beed adopted from mdtraj’s support of the LAMMPSTRJ trajectory format. See https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/lammpstrj.py for details.