scalable molecular simulation

A unified framework for machine learning collective variables for enhanced sampling 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

Unified Free Energy Dynamics (UFED) simulations with OpenMM

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.

Simple tools for obtaining time from biased molecular dynamics simulations

Extended Phase-Space Simulations with OpenMM

A python package for simulating sampling behaviors of enhanced sampling simulations

Deep learning for collective variables.

Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.

Setup and run aMDeNM simulations with Python

Gaussian + LAMMPS + ASE implementation to perform optimization, NEB and metadynamics calculations