Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/simonboothroyd/absolv

Absolute solvation free energy calculations with OpenFF and OpenMM
https://github.com/simonboothroyd/absolv

alchemical free-energy hydration non-equilibrium openff openmm solvation

Last synced: 19 days ago
JSON representation

Absolute solvation free energy calculations with OpenFF and OpenMM

Host: GitHub
URL: https://github.com/simonboothroyd/absolv
Owner: SimonBoothroyd
License: mit
Created: 2021-10-28T17:01:04.000Z (about 3 years ago)
Default Branch: main
Last Pushed: 2024-01-16T13:18:24.000Z (10 months ago)
Last Synced: 2024-01-17T05:31:24.116Z (10 months ago)
Topics: alchemical, free-energy, hydration, non-equilibrium, openff, openmm, solvation
Language: Python
Homepage: https://simonboothroyd.github.io/absolv/
Size: 3.76 MB
Stars: 11
Watchers: 1
Forks: 2
Open Issues: 0
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE

Awesome Lists containing this project

README

ABsolute SOLVantion Free Energy Calculations

Absolute solvation free energy calculations using OpenMM

---

The `absolv` framework aims to offer a simple API for computing the change in free energy when transferring a solute
from one solvent to another, or to vacuum in the case of solvation free energy calculations.

It offers two routes to this end: standard equilibrium calculations and non-equilibrium switching type calculations,
where the latter will be the main focus of this framework.

***Warning**: This code is currently experimental and under active development. If you are using this it, please be
aware that it is not guaranteed to provide correct results, the documentation and testing is incomplete, and the
API can change without notice.*

## Installation

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

```shell
mamba install -c conda-forge absolv
```

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 absolv "openmpi=4.1.5=*external*"
```

## Getting Started

To get started, see the [usage guide](https://simonboothroyd.github.io/absolv/latest/user-guide/overview/).