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Using VMD and NAMD on Mogon

Licensing Issues

We, the ZDV HPC group, will setup and compile VMD and NAMD for you – upon request. You will find the installed modules as

vis/VMD/<version_string>
chem/NAMD/<version_string>

Here, the <version_string> may deviate between the clusters. If you are missing a particular version, please inform us.

Both, VMD and NAMD, come with a license, which prohibits us to just install. We, therefore, need individual users to print and sign the linked licenses (VMD license and NAMD license) on that paper. Subsequently, send it via internal mail (“Hauspost”) to “ZDV HPC group”. We will then set the permissions accordingly.

When doing so, please include:

  • your name
  • your username
  • your email address (in case we need to approach you)

Using VMD

We generally do not provide support in using a particular software with all its flags (or in the case of a GUI, all its clicks). In this particular case we refer to the VMD tutorial.

That being written, we are aware that starting the VMD-GUI can be tricky and the relevant information hard to find.

Starting the graphical user interface (GUI)

Here, we give some brief snippets, covering the essentials:

  • First, we need to load the module and instruct VMD to start in its graphical, non-MPI mode:
$ module load vis/VMD # this will load the most current version, which is installed
$ export VMDNOMPI=1
  • Next, we start an interactive session, e.g. with salloc. Here is a little more information on interactive jobs. With respect to the number of cpus: Not everything in VMD is parallelized. If you want to start an VMD-MPI job, you better write a VMD script and start VMD like a conventional MPI-application.
$ salloc -A <your_account> -p short -c <number_of_cpus> -t <sufficient_time>
<snipping wainting for the session>
$ srun vmd <arguments>
  • When ending the session, do not forget to type exit to relinquish the allocation.

Setting up a simulation files for NAMD

Molecular Dynamics (MD) simulations can be tricky to be set up correctly. It is not unusual to make mistakes, which may consume lots of CPU time. The purpose of these snippets is not to teach running MD simulations in all detail, but to descript how to generate the most basic setup.

The following section refers to the VMD tutorial section on generating a PSF file:

  1. load a new molecule
  2. run the autopsf utility (Extensions → Modeling → Automatic PSF Builder)

This will create the following files: <molecule_prefix>_autopsf_formatted.pdb, molecule_prefix>_autopsf.log, <molecule_prefix>_autopsf.pdb, <molecule_prefix>_autopsf.psf.

Of course, VMD offers many more options, most are more sophisticated than this description.

Using NAMD

With a given configuration file, you can start NAMD like this:

#!/bin/bash
 
#SBATCH -t <time>
#SBATCH -p <partition> # e.g. nodeshort / parallel
#SBATCH -A <account>
#SBATCH -N <rather start with a low number to test>
#SBATCH -n <N * cores / node>
 
module purge
 
module load chem/NAMD
 
# the suffix 'namd_conf' is arbitrary
srun namd2  <prefix>.namd_conf

The configuration file content depends on the simulation to be carried out, however, the coordinates and structure parameters could simply refer to the autogenerated .pdf and .psf files produced by VMD as described, respectively.

namd.txt · Last modified: 2018/08/18 06:12 by meesters