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GROMACS (Application)

Introduction

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 and lipids that have a lot of complicated bonded interactions, but many groups are also using it for research on non-biological systems, e.g. polymers.

Availability Table

Version Default Module Systems
4.5.5 True goblin, orca, redfin
5.0.4 True goblin, orca, redfin, wobbie
5.1.3 True monk
5.1.4 True goblin, orca, redfin, wobbie

Documentation

https://www.sharcnet.ca/help/index.php/GROMACS

Mailing List

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Change Log

o Dec 21, 2016: Installed gromacs/5.1.4 on dusky (for queue submission staff testing).
o Oct 18, 2016: Installed gromacs/5.1.4 on brown, goblin, orca, redfin, saw, wobbie.
o Aug 31, 2016: Installed gromacs/5.1.3 with gpu support on monk.
o Jul 26, 2016: Removed gromacs/5.0.2 from monk.
o Feb 9, 2016: Removed gromacs/4.6.5 from brown, monk, orca, redfin, saw.
o Oct 31, 2015: Removed gromacs/4.5.5 from guppy and mako.
o Feb 11, 2015: Installed gromacs/5.0.4 on saw, brown, orca, hound, goblin, redfin, wobbie. Removed gromacs/5.0.1 and gromacs/5.0.2 from saw, brown, orca, hound, goblin, redfin, wobbie and kraken. Removed gromacs/4.5.4 from brown, goblin, hound, kraken, orca, redfin and saw. Removed gromacs/4.6.1 from bro, hound, monk, orca, redfin and saw. Removed gromacs/4.0.5 from guppy and mako.
o Dec 5, 2014: Installed gromacs/5.0.2 on monk (gpu); brown, saw (xeon); goblin, hound, kraken, orca redfin, wobbie.
o Sep 30, 2014: Installed gromacs/5.0.1 on brown (intel binary), goblin, hound, kraken, orca, redfin, saw (intel binary) and wobbie.
o Jan 16, 2014: Installed gromacs/4.6.5 on brown, hound, monk (gpu), orca, redfin, saw.
o Jul 05, 2013: Installed gromacs/4.6.1 on monk.
o May 22, 2013: Installed gromacs/4.6.1 on brown, hound, orca, redfin and saw.
o Feb 22, 2012: Installed gromacs/4.5.5 on angel, brown, goblin, gulper, guppy, hound, kraken, mako, orca, redfin, saw. Removed 4.5.1 from remaining systems: saw, redfin, angel.
o Jun 22, 2011: Removed version 4.5.1 from angel, brown, goblin, guppy, hound, kraken, mako, rainbow and requin. Installed version 4.0.5 on gulper and orca.
o Apr 19, 2011: Installed 4.5.4 on angel, brown, goblin, guppy, hound, kraken, mako, orca, gulper.