.. _simulators:

.. image:: /docs/images/galileo_pres.png

Simulation Software in Galileo
===============================

Galileo supports a variety of molecular dynamics software.

ACEMD3
--------

`ACEMD Platform <https://www.acellera.com/products/molecular-dynamics-software-gpu-acemd/>`_
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
----------

`AmberTools <https://ambermd.org/AmberTools.php>`_ 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.

`Galileo Tutorial Link <docs/ambertools-batch-public.html>`_

AutoDock Vina
--------------

`AutoDock Vina <http://vina.scripps.edu/>`_ 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.

`Galileo Tutorial Link <docs/autodock-vina-batch-public.html>`_

Gromacs
-------

`Gromacs <https://www.gromacs.org/>`_  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.

`Galileo Tutorial Link <docs/gromacs-batch-public.html>`_