VMD

VMD (Visual Molecular Dynamics)[1] is a molecular visualization program with 3-D graphics and built-in scripting for displaying, animating, and analyzing large bimolecular systems.

Important Notes

- Request the sufficient memory and number of processors for your job. Refer to HPC Batch Job & Interactive Job Submissions.
- Batch job is preferred over Interactive unless you really want to visualize your output.
- If you have GUI intensive job, refer to HPC GUI Visual access.

Installed Versions

All the available versions of VMD for use can be viewed by issuing the following command. This applies for other applications as well.

module avail vmd

output:

---------------------- /usr/local/share/modulefiles -------------------------

vmd/1.9.1 (D) vmd/1.9.2

The default version is identified by "(D)" behind the module name and can be loaded as:

module load vmd

The other versions of VMD can be loaded as:

module load vmd/<version>

Running VMD

Batch Job

Example: RMSD (Root Mean Square Deviation) calculation for plx3 molecule

Copy the directory (plx3) containing the input and job files from /usr/local/doc/VMD to your home directory

cp -r /usr/local/doc/VMD/plx3 .

Go to the plx3 directory

cd plx3

The content of the job file "job.slurm" is showed below:

#!/bin/bash

#SBATCH --time=00:10:00

#SBATCH -N 1 -n 4

#SBATCH -J VMDtest

module load vmd

cp chtr.psf chtr3.dcd rmsf-plx3.tcl $PFSDIR

cd $PFSDIR

NPROCS=$SLURM_NPROCS

vmd chtr.psf chtr3.dcd -dispdev text -eofexit < rmsf-plx3.tcl

cp -r * $SLURM_SUBMIT_DIR

Submit the job

sbatch job.slurm

Find the output file " rmsfCA-PLX3-aligned.txt" containing the values.

output:

...

5.041041374206543

5.034134387969971

4.919175148010254

4.883508682250977

5.126375675201416

Interactive Job

1. Type:

srun --x11 -N 1 -n 12 --mem=5gb --pty bash

(This will assign you any one of the available compute nodes in the cluster). For better visual access, visit HPC Visual Access guide.

2. Set vmd environment by loading the module

module load vmd

Go to plx3 directory

cd plx3

3. Type:

vmd chtr.psf chtr3.dcd

You will see the GUI as showed:

To run vmd on multiple processors interactively, request the nodes and processors as follows. Your job may want more than 10 hours of default wall time, so assign that accordingly with walltime keyword. Refer to Batch and Ineractive Job Submission guide for details.

srun --x11 -N <n> -n <p> --mem=<m>gb --pty bash

(Note: replace <n>, <p>, and <m> with number of nodes and processor per node, and memory value respectively that you want to request)

Running VMD in GUI Mode Using Special Graphics Interface

For better visualization experience, please refer to HPC Visual Access to request a compute node. We then access to the folder plx3 in our home folder: