md-simulations

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.

A Streamlit-based app for post-MD analyses and visualization of GROMACS simulation trajectories.

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

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

A QM-MM Tutorial of Enzyme Reaction Dynamics

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

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"

A command-line tool for computing radial distribution functions (RDFs) from molecular dynamics trajectories in XYZ format, powered by OVITO.

Step-by-step GROMACS workflow for protein-ligand complex molecular dynamics simulations