Development version of plumed 2

Collective variables library for molecular simulation and analysis programs

scalable molecular simulation

A unified framework for machine learning collective variables for enhanced sampling simulations

Software Suite for Advanced General Ensemble Simulations

Python Suite for Advanced General Ensemble Simulations

Weighted Ensemble simulation framework in Python

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

Enhanced protein mutational sampling using time-lagged variational autoencoders

Using supervised machine learning to build collective variables for accelerated sampling

Unified Free Energy Dynamics (UFED) simulations with OpenMM

🦜 DISCOTRESS 🦜 is a software package to simulate and analyse the dynamics on arbitrary Markov chains

Using neural networks for enhanced sampling in computational biophysics

Useful Collective Variables for OpenMM

asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.

An OpenMM plugin for slicing nonbonded interactions based on particle classification

Permutationally invariant networks for enhanced sampling (PINES)

Machine Learning Transition State Analysis (MLTSA) suite with Analytical models to create data on demand and test the approach on different types of data and ML models.

Simple tools for obtaining time from biased molecular dynamics simulations