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
#$ -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