AToM-OpenMM¶

The Alchemical Transfer Method for OpenMM (AToM-OpenMM) is an extensible Python package for estimating absolute and relative binding free energies of molecular complexes.

AToM-OpenMM implements the Alchemical Transfer Method (ATM) with asynchronous parallel replica exchange molecular dynamics using OpenMM. It can be deployed on workstations or cluster nodes with one or more GPUs.

This version uses ATMForce, available in OpenMM 8.4.0 and later.

Start Here¶

Installation: install AToM-OpenMM and its runtime dependencies.
Tutorials: start with Colab notebooks or local repository tutorials.
User guide: learn the high-level ABFE and RBFE workflow layout.
Theory: introduces the theory of the Alchemical Transfer approach
API reference: find command-line entry points, workflow modules, and utility modules.

Credits¶

AToM-OpenMM is developed and maintained by Emilio Gallicchio's lab, with support from current and past grants from the National Science Foundation and the National Institutes of Health.

Maintainer and author:

Emilio Gallicchio

Contributors:

Elian Tiudic
Sylvester Sakyi
Stefan Doerr
Sheenam Khuttan
Joe Z Wu
Solmaz Azimi
Baofeng Zhang
Rajat Pal

The asynchronous replica exchange method was first implemented in the AsyncRE package for the IMPACT program.

Citations¶

Please cite AToM-OpenMM if you use this software in your research.

License¶

AToM-OpenMM is research software under active development. It is provided without guarantees of correctness.