https://github.com/Psivant/femto

A comprehensive toolkit for predicting free energies
https://github.com/Psivant/femto

Last synced: 26 days ago
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A comprehensive toolkit for predicting free energies

• Host: GitHub
• URL: https://github.com/Psivant/femto
• Owner: Psivant
• License: mit
• Created: 2023-12-07T15:28:18.000Z (7 months ago)
• Default Branch: main
• Last Pushed: 2023-12-22T16:45:14.000Z (6 months ago)
• Last Synced: 2024-01-14T02:49:11.069Z (6 months ago)
• Language: Python
• Homepage: https://psivant.github.io/femto/
• Size: 1.32 MB
• Stars: 33
• Watchers: 1
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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• awesome-stars - Psivant/femto - A comprehensive toolkit for predicting free energies (Python)

README

        
Free Energy and MD Toolkit using OpenMM


A comprehensive toolkit for predicting free energies




  

    

  

  

    

  

  

    

  



---

The `femto` framework aims to offer not only a compact and comprehensive toolkit for predicting binding free energies

using methods including `ATM` and `SepTop`, but also a full suite of utilities for running advanced simulations using

OpenMM, including support for HREMD and REST2.

_**Warning:** The ATM implementation was recently updated to make use of the new `ATMForce` shipped with OpenMM 8.1.

While every effort was made to ensure correctness, this was a major change that is still being tested and there may

be bugs. Please report any issues you encounter._

_Further, the default protocols selected for the ATM and SepTop methods are still being tested and optimized, and may

not be optimal. It is recommended that you run a few test calculations to ensure that the results are reasonable._

## Installation

This package can be installed using `conda` (or `mamba`, a faster version of `conda`):

```shell

mamba install -c conda-forge femto

```

If you are running with MPI on an HPC cluster, you may need to instruct conda to use your local installation

depending on your setup

```shell

mamba install -c conda-forge femto "openmpi=4.1.5=*external*"

```

where in this example you should change `4.1.5` to match the version of OpenMPI installed on your cluster / machine.

## Getting Started

To get started, see the [usage guide](https://psivant.github.io/femto/latest/guide-md).

## Acknowledgements

This framework benefited hugely from the work of Psivant's [Open Science Fellows](https://psivant.com/company/open-science-fellows/).

### ATM

The ATM implementation is based upon the work and advice of E. Gallicchio _et al_:

* [Wu, Joe Z., et al. "Alchemical transfer approach to absolute binding free energy estimation." Journal of Chemical Theory and Computation 17.6 (2021): 3309-3319.](https://pubs.acs.org/doi/10.1021/acs.jctc.1c00266)

* [Azimi, Solmaz, et al. "Relative binding free energy calculations for ligands with diverse scaffolds with the alchemical transfer method." Journal of Chemical Information and Modeling 62.2 (2022): 309-323.](https://pubs.acs.org/doi/full/10.1021/acs.jcim.1c01129)

### SepTop

The SepTop implementation is based upon the work and advice of H. M. Baumann, D. L. Mobley _et al_:

* [Rocklin, Gabriel J., David L. Mobley, and Ken A. Dill. "Separated topologies—A method for relative binding free energy calculations using orientational restraints." The Journal of chemical physics 138.8 (2013).](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598757/)

* [Baumann, Hannah M., et al. "Broadening the scope of binding free energy calculations using a Separated Topologies approach." Journal of Chemical Theory and Computation 19.15 (2023): 5058-5076.](https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00282)