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 --ntasks=1        # (or -n 1) Request 1 core
#SBATCH --mem-per-cpu=1G  # Request 1GB RAM per core (1GB total)
#SBATCH --time=1:0:0      # (or -t 1:0:0) Request 1 hour runtime

module load vmd

vmd -dispdev text -e example.vmd

References

• VMD website
• VMD documentation