Installation Guide

Welcome to the installation guide for wepy. Follow the steps below to set up the environment and install wepy.

Prerequisites

Ensure that you are using Python 3.10. It is recommended to set up a conda environment for managing dependencies and ensuring compatibility.

conda create -n wepy-env python=3.10
conda activate wepy-env

You can install wepy from the latest git repository.

Installing from Git (for the latest version):

pip install git+https://github.com/ADicksonLab/wepy.git

To install OpenMM, which is highly recommended for running molecular dynamics simulations:

conda install -c conda-forge openmm=8.0.0

If the conda version of openmm doesn’t work for your compute environment, consult the OpenMM documentation.

The mdtraj library is used by wepy to create and manipulate system topologies. It can also be installed via conda:

conda install -c conda-forge mdtraj=1.9.9

These version numbers work correctly at the time of this writing and avoid some incompatibility issues with numpy and pandas dependencies.

After installation, you should be able to import wepy in python. Verify it by running:

python -c "import wepy"

If the installation was successful, you should not see any errors.