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.

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