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SW:GROMACS

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GROMACS

Description

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. - Homepage: http://www.gromacs.org

Access

Loading the Module

There are a variety of GROMACS modules supported on Ada and Terra. Currently, the latest version supported is GROMACS 2016.4, and is available on the Ada and Terra clusters. For more information, see our modules page.
It is simplest to follow along using the exact same modules used in the examples below.

To purge unnecessary modules before getting started:

 [ netID@cluster ~]$ module purge

To see all versions of GROMACS available on Ada or Terra:

 [ netID@cluster ~]$ module spider GROMACS

To load a particular version of GROMACS on Ada or Terra (Example: 5.1.4):

 [ netID@cluster ~]$ module load GROMACS/5.1.4-foss-2016b-mt

NOTE: Pay close attention to the information following the version number of the module. This is called the toolchain. This information describes what other modules will be loaded with GROMACS. These modules will be disrupted by use of extraneous modules of different toolchains, so please purge all unnecessary modules prior to using GROMACS.

Usage on the Login Nodes

Please limit interactive processing to short, non-intensive usage. Use non-interactive batch jobs for resource-intensive and/or multiple-core processing. Users are requested to be responsible and courteous to other users when using software on the login nodes.

The most important processing limits here are:

•ONE HOUR of PROCESSING TIME per login session.
•EIGHT CORES per login session on the same node or (cumulatively) across all login nodes.

Anyone found violating the processing limits will have their processes killed without warning. Repeated violation of these limits will result in account suspension. Note: Your login session will disconnect after one hour of inactivity.