Bioinformatics Tools

NAMD is a parallel molecular dynamics code for large biomolecular systems.

CHARMM (Chemistry at HARvard Molecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Accelrys provides simulation and informatics software for researchers working in drug discovery and the development of chemicals and materials

The Amber Molecular Dynamics Package. Amber is a package of programs for molecular dynamics simulations of proteins and nucleic acids

MacKerell Laboratory: empirical force field parametrization

swissparam:This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.