AlphaFold 3 inference pipeline.

The Charm++ parallel programming system. Visit https://charmplusplus.org/ for more information.

Molfileplugin for VMD that lets me read in GROMACS tpr files

Umbrella Integration of PMF calculations - 1D & 2D

Python implementation of the umbrella integration method for potential of mean force (PMF) calculations

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and…

Code to reproduce results and figures of Klimek et al EPJE 2025

Timewarp is a research project using deep learning to accelerate molecular dynamics simulation.

This is a collection of answers to a SM book Statistical Mechanics Theory and Molecular simulation written by Mark E. Tuckerman. Lecture notes can be added too.

This repo contains CUDA-Q Academic materials, including self-paced Jupyter notebook modules for building and optimizing hybrid quantum-classical algorithms using CUDA-Q.

Replica-exchange tools for NAMD

Implementation of the hybridMC-MetaD algorithm and usage examples

Detect and characterize binding pockets from molecular simulations.

Weighted Ensemble simulation framework in Python

Fokker-Planck Score Learning: Efficient Free-Energy Estimation under Periodic Boundary Conditions

TS-DAR tutorials. The TS-DAR code is here: https://github.com/xuhuihuang/ts-dar

TS-DAR identifies transition states of protein conformational changes from MD simulations using hyperspherical embeddings in the latent space.

Simulation and Generalized Langevin Equation Study of Lipid Subdiffusion in Biomembrane Phases

Force-field-enhanced Neural Networks optimized library

A program for filling up the missing part of protein structure