Gromacs GRO file reader

../../../_images/gromacs_reader.png — 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=False)

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 (bool) – Activates the generation of ad-hoc bonds connecting the atoms loaded from the file. Ad-hoc bond generation is based on the van der Waals radii of the chemical elements. Alternatively, you can apply the CreateBondsModifier to the system after import, which provides more control over the generation of pair-wise bonds.