1. Installation

This document should help you to install the GromacsWrapper package. Please raise and issue in the Issue Tracker if problems occur or if you have suggestions on how to improve the package or these instructions. Ask for help in the discussions forum.

1.1. `pip` installation

The latest release can be directly installed with pip:

pip install GromacsWrapper

(This will automatically download and install the latest version of GromacsWrapper from PyPi.)

1.2. `conda` installation

New in version 0.8.1.

Changed in version 0.8.3: Package migrated from bioconda to conda-forge.

Install as a conda-forge package with the conda package manager from the conda-forge channel

conda install -c conda-forge gromacswrapper

The conda-forge channel should be explicitly specified if you are not already using it by default.

Note

The conda-forge channel also contains conda-forge packages for GROMACS (earlier versions ≤ 2021.x are available as GROMACS bioconda packages), which can be used for testing and system setup; for running in a high-performance environment you are advised to carefully benchmark and possibly compile a version of GROMACS that is tuned for the system.

1.3. Manual Download

If your prefer to download manually, get the latest stable release from https://github.com/Becksteinlab/GromacsWrapper/releases and either

pip install GromacsWrapper-0.8.5.tar.gz

or install from the unpacked source:

tar -zxvf GromacsWrapper-0.8.5.tar.gz
cd GromacsWrapper-0.8.5
pip install .

1.4. Source code access

The tar archive from https://github.com/Becksteinlab/GromacsWrapper/releases contains a full source code distribution.

In order to follow code development you can also browse the code git repository at https://github.com/Becksteinlab/GromacsWrapper and checkout the main branch:

git clone https://github.com/Becksteinlab/GromacsWrapper.git
cd GromacsWrapper

Code contributions are welcome. We use black for uniform code formatting so please install black and run it on your code.

1.5. Requirements

Python >= 3.8 and GROMACS (4.6.x, 2016, 2018, 2019, 2020, 2021, 2022, 2023) must be installed.

1.5.1. System requirements

Tested with Python 3.8–3.12 on Linux and Mac OS X. Earlier Python versions were only supported until release 0.8.5.

1.5.2. Required Python modules

The basic package makes use of numpy and numkit (which uses scipy); all dependencies are installed during a normal installation process.