MDAnalysis

Overview

MDAnalysis is a program to

Version 0.19.2 is installed on the CSF and is part of the anaconda3 installation.

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

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load the anaconda python:

module load apps/anaconda3/5.2.0/bin

Running the application

Include the following in your python code

import MDAnalysis

Please do not run MDAnalysis jobs on the login node. Jobs should be submitted to the compute nodes via batch.

Please refer to the CSF Anaconda Python documentation for further guidance.