gmx-top4py

GROMACS topology files for python

!!!!!!!!!!!!!!!!!!!!!! DEPRECATED !!!!!!!!!!!!!!!!!!!!!!!!
This projected has been renamed to gmxtop.
Please use pip install gmxtop instead.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Description

The gmx-top4py project provides a python interface to

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

The gmx-top4py 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 gmx-top4py 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 gmx-top4py
• Advanced tutorial - Advanded accessing of topology information with gmx-top4py
• Force field parameter tutorial - Adapting force field parameters with gmx-top4py

Installation

From PyPI

pip install gmx-top4py

From source via uv

Clone repository and move into

git clone git@github.com:graeter-group/gmx-top4py.git
cd gmx-top4py

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/gmx-top4py.git
cd gmx-top4py

Install repository into conda environment

conda create -n gmx-top4py python -y
conda activate gmx-top4py
pip install -e '.[dev]' # install with dev dependencies

Verify install by running the tests

pytest tests