Installation

It is recommended that the installation is performed in a personal python environment (miniforge, miniconda, conda, or similar). AToM-OpenMM requires the openmm, configobj and numpy python modules.

Runtime Environment

This version of AToM-OpenMM requires OpenMM 8.4.0 or later. This conda command installs the necessary requirements:

mamba create -n atm8.4.0 -c conda-forge 'openmm>=8.4' ambertools openmmforcefields configobj setproctitle r-base espaloma
mamba activate atm8.4.0

setproctitle above is optional but useful to track the names of the processes started by AToM-OpenMM. The ambertools, openmmforcefields, and espaloma packages are not actual dependencies; they are used to setup the molecular systems. openmmforcefields, in particular, is used to assign force field parameters using OpenFF, GAFF, or espaloma. espaloma is a machine-learning system by the Chodera lab to assign force field parameters. r-base with the UWHAM R package (see below) is required for free energy estimation. See examples for examples and tutorials.

Install AToM-OpenMM

Install the latest release:

pip install atom-openmm

Or install from source:

git clone https://github.com/Gallicchio-Lab/AToM-OpenMM.git
cd AToM-OpenMM
pip install .

Install UWHAM for free energy estimation:

Rscript -e 'install.packages("UWHAM", repos = "http://cran.us.r-project.org")'