MDAnalysis

Overview

MDAnalsysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations.

Version 0.8.1 and 0.17.0 are available on the CSF.

Restrictions on use

There are no restrictions on accessing MDanalysis on the CSF. The source is released under the GNU GPL v2 license.

All users should cite their use of the software as per the MDAnalysis website.

Set up procedure

To access the software you must first load one of the following modulefile:

Version 0.8.1 of MDAnalysis is available directly from the anaconda python suite version 1.9.1

module load apps/binapps/anaconda/1.9.1

Version 0.17.0 is available as it’s own modulefile on the CSF and it will automatically load anaconda python version 3/4.20 for you.

module load apps/gcc/python-packages/anaconda3-4.2.0/mdanalysis/0.17.0

Running the application

Please do not run MDAnalysis on the login node. Jobs should be submitted to the compute nodes via batch. Please see the CSF anaconda python documentation for example job scripts.