VMD

Visual Molecular Dynamics (VMD) is designed for modelling, visualisation and analysis of biological systems such as proteins and nucleic acids.

VMD is available as a module on Apocrita.

Usage

To run the default installed version of VMD, simply load the vmd module:

$ module load vmd
vmd

For full usage documentation, run vmd --help.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G   # Request 1GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load vmd

vmd -dispdev text -e example.vmd

References

• VMD website
• VMD documentation