MEMBPLUGIN: studying membrane complexity in VMD
A fast and versatile molecular dynamics program
Command-line tools for analyzing Amber Molecular Dynamics simulations.
Designed for coarse-grained protein association simulations
Visual and Insitu Analytics for Molecular Interactive Simulation
PYthon eXtension for Ab Initio Dynamics
Newtonian dynamics near the crossing seam
Interpretation of Biomolecular MD simulations
Molecular dynamics with aqueous-organic solvent mixtures
Locally-Scaled Diffusion Maps from molecular dynamics trajectories
Graphic molecular dynamic package.
Molecular Dynamics Analyzer (MDA)
Differential activE sub-Network (DEN): R/Bioconductor based package
Python script to automate umbrella sampling with AMBER
Initial system (box) generator for biological molecular simulations
Polymer simulation utilites
Hydrogen/deuterium exchange estimation for isotopic fine structure MS