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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.


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

$ module load 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:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load vmd

vmd -dispdev text -e example.vmd