GENESIS (GENeralized-Ensemble SImulation System) is a molecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes.
SINDO is a suite of programs to carry out anharmonic vibrational structure calculations. It consists of programs for generating the anharmonic potential energy surface (MakePES), vibrational self-consistent field (VSCF) and post-VSCF solver (FSindo), and a visualizer (JSindo). SINDO is licensed under GNU General Public License v3.0, and is available free of charge.
A MATLAB/Octave toolbox for statistical analysis of molecular dynamics trajectories.
An interface program for multi-dimensional replica-exchange molecular dynamics (MREMD) simulations.