Gromacs GRO file reader — OVITO User Manual 3.16.0 documentation

# 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=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.