Simulation Software in Galileo¶
Galileo supports a variety of molecular dynamics software.
ACEMD Platform is a complete and fast solution package, designed to run and analyze your molecular dynamics (MD) simulations. It includes ACEMD, Parameterize and HTMD packages. ACEMD is the MD engine that runs the simulation, Parameterize is a force field parameterization tool for small molecules and HTMD is a Python package that you can use to create systems, prepare them and, once ACEMD has finished simulating those systems, analyze their trajectories.
AmberTools consists of several independently developed packages that work well by themselves, and with Amber20 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute.
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.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.