INSTALL.rst

Quick installation instructions for MDPOW

MDPOW is compatible with Python 3.7+ and tested on Ubuntu and Mac OS.

We recommend that you install MDPOW in a virtual environment.

Installation for users

Most users should follow these instructions.

We use the Anaconda distribution with the conda command to manage dependencies (see installing the Anaconda distribution for details on how to set up conda).

To run MDPOW you will also need to install a compatible version of GROMACS.

Conda environment with pre-requisites

Make a conda environment with the latest packages for Python 3.7 and higher with the name mdpow; this installs the larger dependencies that are pre-requisites for MDPOW:

conda create -c conda-forge -n mdpow  numpy scipy matplotlib mdanalysis pyyaml 'pandas>1.3.0'
conda activate mdpow
pip install gromacswrapper

Install MDPOW with pip:

pip install mdpow

(This will install additional dependencies such as alchemlyb, which in turns needs pandas > 1.3.0.)

Installation from source

Instead of the pip-installation of MDPOW, you can also install from source:

conda activate mdpow
git clone https://github.com/Becksteinlab/MDPOW.git
pip install ./MDPOW

(Older releases are available but outdated; use the latest source for now.)

Checking that the installation worked

Check that you can run the mdpow-* commandline tools:

mdpow-equilibrium --help

should print a whole bunch of messages. If your GROMACS installation cannot be found, make sure you source GMXRC or load the appopriate modules or whatever else you have to do so that the gmx command is found. See https://gromacswrapper.readthedocs.io for more details.

Check that you can import the module:

python
>>> import mdpow
>>> help(mdpow)

In case of problems file an issue at https://github.com/Becksteinlab/MDPOW/issues

Developer installation

A development install is useful while hacking away on the code:

cd MDPOW
pip install -e  .