In this example we will use “alp” test from Amber’s test suite. To get the files relevant to this example:

$ module add examples
$ example get Amber
$ cd Amber && ls

amber.pbs  coords  md.in  prmtop  README.md

Examine the batch script amber.pbs, and adjust the names of the files i.e. input and coordinates files. Also, adjust the number of nodes, processors per node and walltime. To submit the job:

qsub amber.pbs 

Results will be saved in the md.out file (in our example).