How to analyze molecular dynamics data with PyEMMA

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

Simulation-Enabled Estimation of Kinetic Rates - Version 2

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.

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

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

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

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.

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

Scirpts used for Metainference MD Simulations

The simplest usage of the API, $theme: mat.define-theme() defines a theme with default values.