VMD

Install pre-compiled Version of VMD

Download pre-comiled text-mode vmd.

$ cd $HOME/tmp
$ wget http://spack.pi.sjtu.edu.cn/mirror/vmd/vmd-1.9.3.bin.LINUXAMD64.text.tar.gz

Extract the tar.

$ cd $HOME/tmp
$ tar xzvpf vmd*.tar.gz

Configure installation directories.

$ cd $HOME/tmp
$ mkdir -p $HOME/vmd-1.9.3-textmode/bin
$ export VMDINSTALLBINDIR="$HOME/vmd-1.9.3-textmode/bin" 
$ mkdir -p $HOME/vmd-1.9.3-textmode/lib
$ export VMDINSTALLLIBRARYDIR="$HOME/vmd-1.9.3-textmode/lib" 
$ cd vmd-1.9.3
$ ./configure

Install vmd.

$ cd ~/tmp/vmd-*/src/
$ make install

Check if vmd has been installed sucessfully.

$ $HOME/vmd-1.9.3-textmode/bin/vmd -h

Submit the following job script vmd.slurm to SLURM job scheduling system via sbatch -p cpu vmd.slurm.

#!/bin/bash

#SBATCH --job-name=vmd
#SBATCH --partition=cpu
#SBATCH --mail-type=end
#SBATCH --mail-user=YOU@EMAIL.COM
#SBATCH --output=%j.out
#SBATCH --error=%j.err
#SBATCH -p cpu
#SBATCH -n 1
#SBATCH --exclusive

ulimit -l unlimited
ulimit -s unlimited

$HOME/vmd-1.9.3-textmode/bin/vmd YOUR VMD OPTIONS

Reference