gmxtop

GROMACS topology files for python

Description

The gmxtop project provides a python interface to

• read and write toplogy and force field information from GROMACS-type top-files
• alter force field parameters

The gmxtop project derives this functionality from the kimmdy project, originally developed by the graeter-group, and includes only minor modifications to parts of the original code to operate independently. The kimmdy project is licensed under the GNU General Public License v3.0 and, as a derivative work, the gmxtop project is distributed under the same license. See LICENSE for details.

Limitations

• CMAP corrections ([ cmaptypes ], [ cmap ]) are only passed through: they are read and written back unchanged, but not parsed into objects. Hence, CMAP terms are not generated for new residues and their atom numbers are not updated when atoms are renumbered.
• CHARMM force field files use #ifdef/#ifndef statements within sections (e.g. #ifdef HEAVY_H in [ atomtypes ]). This is not supported yet. Thus, CHARMM topologies can not be read directly. As a workaround, preprocess the topology with grompp first and use the resulting standalone topology:

gmx grompp -f empty.mdp -c conf.gro -p topol.top -pp topol_pp.top

Tutorials

The following tutorials are avaiable as Google Colab notebooks and hence do not require a local installation:

• Basic tutorial - Basic accessing of topology information with gmxtop
• Advanced tutorial - Advanded accessing of topology information with gmxtop
• Force field parameter tutorial - Adapting force field parameters with gmxtop

Installation

From PyPI

pip install gmxtop

From source via uv

Clone repository and move into

git clone git@github.com:graeter-group/gmxtop.git
cd gmxtop

Install repository

uv sync

Activate virtual environment

source .venv/bin/activate

Verify install by running the tests

pytest tests

From source via conda and pip

Clone repository and move into

git clone git@github.com:graeter-group/gmxtop.git
cd gmxtop

Install repository into conda environment

conda create -n gmxtop python -y
conda activate gmxtop
pip install -e '.[dev]' # install with dev dependencies

Verify install by running the tests

pytest tests