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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 latest 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 for VMD using 1 core with 1G memory.

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_vmem=1G
#$ -l h_rt=1:0:0
#$ -N vmd_serial_test

module load vmd

vmd -dispdev text -e example.vmd

References