UMMAP

Overview

UMMAP is a trajectory analysis package for molecular dynamics type simulations, capable of working with several leading MD codes.

Restrictions on use

This software is not open source.

It is only to be used for academic purposes. No commercial use is permitted. The license defines academic purposes as:

• “fundamental or basic research or academic teaching,including any fundamental research that is funded by any public or charitable body, but not any purpose that generates revenue (as opposed to grant income) for the Licensee or any third party. Any research that is wholly or partially sponsored by any profit making organisation or that is carried out for the benefit of any profit-making organisation Is not an Academic Purpose”

No source or object code is available.

In any published work produced by users which includes results achieved by using the UMMAP software, users must acknowledge that the UMMAP software was used in producing the information in such publication.

The software is licensed until 18th March 2023.

Please note that the version labelled 2.7411 has been removed as it is no longer licensed.

A full copy of the license, which all users should read before using the software, is available in $UMMAP_HOME/LICENCE.PDF .

To request access to UMMAP please email its-ri-team@manchester.ac.uk and include an acknowledgement that your work will be in line with the T&Cs. If you would like to see a full copy of the license first we can send one to you.

Set up procedure

To load the UMMAP module you will first need to be added to the ummap group. To load the module type:

module load apps/binapps/ummap/2.20.5

Please note, we now recommend loading module files in your jobscript rather than on the login node.

The software was compiled with Intel 18, the required compiler modulefile will be automatically loaded for you.

Please note that the version labelled 2.7411 has been removed as it is no longer licensed.

Running the application

The software is launched using the command ummap

Batch Usage

To run UMMAP in a batch job, create a jobscript similar to the following:

#!/bin/bash --login
#$ -cwd
module load apps/binapps/ummap/2.20.5

ummap -f "trajectory.vtf" -t FIRST 5 –g ALK OH -m C -o DATASET  

Submit your job to the batch system using

qsub myjobscript

where myjobscript is the name of your jobscript file.

Please note UMMAP is a serial only code, so you should not specify a #$ -pe flag in your jobscript.

Further info

The UMMAP website has some additional info.
The user manual is available in $UMMAP_HOME/UMMAP_Manual.pdf.