xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs
-
Updated
Nov 14, 2023 - Python
xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs
[early prototype testing] An interactive point-and-click text interpreter with logic in python and UI in your browser.
This repo contains a python script to obtain solvent sites according to https://watclust.wordpress.com/methodology/ using as input molecular dynamics in AMBER format (https://ambermd.org/).
Molecular Dynamics - Simulation Analysis and Preparation Suite
Python-based softwares for QM and MD data extraction.
A Snakemake workflow for analyzing AMBER molecular dynamics simulations.
This code adds custom-made amino acids to the GROMACS forcefield directory.
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.
A Package for Parametrization of Molecular Mechanics Force Fields
A command line application to launch molecular dynamics simulations with OpenMM
A project (and object) for storing, manipulating, and converting molecular mechanics data.
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
Add a description, image, and links to the amber topic page so that developers can more easily learn about it.
To associate your repository with the amber topic, visit your repo's landing page and select "manage topics."