How to analyze molecular dynamics data with PyEMMA

Rapid Generation of Rare Event Pathways Using Direction Guided Adaptive Sampling: From Ligand Unbinding to Protein (Un)Folding

Simulation-Enabled Estimation of Kinetic Rates - Version 2

MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation technique with coordinate-based particles). It can be used on a script layer or as an interactive plugin for PyMol. Features are different selection modes and Optimizers to distribute restraints.

This code adds custom-made amino acids to the GROMACS forcefield directory.

Molecular dynamics simulation of nano Structures, Materials and Properties using LAMMPS software.

A Python package that aims to characterise the dynamics of local chemical environments from Molecular Dynamics trajectories of proteins and other biomolecules. Public mirror of https://gitlab.jsc.fz-juelich.de/slbio/speadi.

Tools for running MD simulations in OpenMM

Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.

Analysis tool for H5MD file (HDF5 format for molecular dynamics simulation data)

A mesh free molecular dynamics (MD) simulation for a fluid in an isothermal container

A QM-MM Tutorial of Enzyme Reaction Dynamics

sbm-tools is a simple python package for creating, modifying, and maintaining input files for native Structure-Based Model simulations to be used with the popular simulation software GROMACS.

This repo contains the data from: EVCouplings, DynaMut2, MDM-TASK, MD simulation. These files are important for understanding book chapter 17 "Computational Methods to Engineer Cas Proteins for Efficient Genome Editing"

Plots the results generated by Schrodinger's Desmond Simulation Suite

🔬 pyProCT (Python 3 fork) brings the original pyProCT clustering toolkit back to life under modern Python. ⚙️ This version fixes Python 2 legacy issues, updates Cython extensions, adapts to recent NumPy/SciPy APIs, and ensures all clustering algorithms and postprocessing actions work end-to-end.

xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs

End-to-end AMBER protocol to simulate N-acylated peptides (lipopeptides) in bacterial membranes using Lipid21 & PACKMOL-Memgen.