Gromacs GRO file reader

User interface of the Gromacs GRO file reader, which appears as part of a pipeline’s file source.

This file format is used by the GROMACS molecular dynamics code. A format specification can be found here.

Important

The file reader automatically converts atom coordinates and cell vectors from nanometers to Angstroms during import into OVITO, multiplying all values by a factor of 10.

Python parameters

The file reader accepts the following optional keyword parameters in a call to the import_file() or load() Python functions.

import_file(location, centering=True, generate_bonds='off')

Parameters:

• centering (bool) – If set to True, the simulation cell and all atomic coordinates are translated to center the box at the coordinate origin. If set to False, the corner of the simulation cell remains fixed at the coordinate origin.

• generate_bonds (str) – Controls the generation of interatomic bonds during the file import process. The bond criterion can be based on the van der Waals radii of the chemical elements ('vdw'), on their covalent radii and maximum coordination numbers ('covalent'), or on the built-in table of element-pair bond distances adopted from the VESTA program ('vesta'). 'off' disables bond generation. These criteria correspond to the modes of the CreateBondsModifier, which you can alternatively apply to the system after import for more control over the generation of bonds.

Changed in version 3.17.0: The generate_bonds parameter now selects the bond criterion. True is still accepted as an alias for 'vdw'.