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

Python Suite for Advanced General Ensemble Simulations

Software Suite for Advanced General Ensemble Simulations

Weighted Ensemble simulation framework in Python

Unified Free Energy Dynamics (UFED) simulations with OpenMM

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

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

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asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax. Computationally costly operations can be performed locally or submitted to a queuing system.

Useful Collective Variables for OpenMM

Using neural networks for enhanced sampling in computational biophysics

An OpenMM plugin for slicing nonbonded interactions based on particle classification

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.

Files for PLUMED Masterclass-22-11

Simple tools for obtaining time from biased molecular dynamics simulations