Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. Output of a few of these include graphics; the cluster nodes do not generally have interactive graphics, so any graphics you produce with an Amber program should be saved to a file that you can review later.

To load the Amber environment, type:

module load amber

You can put any setup commands into a script. The following script runs the jac benchmark mentioned on the Amber home page on nyx. This benchmark is for dihydrofolate reductase (159 residue protein) in TIP3P water (23,558 total atoms). PME is used for electrostatics, and van der Waals interactions are truncated at 9 Ang.

Once you have a script (like bnch.jac below) for your problem, you can create a PBS script and submit that to the cluster. For a full example copy $AMBERHOME/jac2 to your /home/your-user-name
: cp -r $AMBERHOME/jac2 /home/your-user-name
Read the bnch.jac you've copied; you can use it to drive sander or psander or pmemd. Then edit and submit the following script:

#PBS -N amber-job
#PBS -S /bin/csh
#PBS -q route
#PBS -l nodes=1:ppn=4,mem=1gb,walltime=1:00:00
#PBS -M your-email-address
#PBS -m abe
#PBS -V
#
echo "I ran on:"
cat $PBS_NODEFILE
#
#cd to your execution directory first
cd /home/your-user-name
setenv TESTsander pmemd
setenv DO_PARALLEL "mpirun -np 4"
#
#
./bnch.jac

The items in bold should be changed to suit you and your task. If you save that script with, for example, the name jac.pbs (choose a name that has some meaning for you) you can then submit it with the command:

qsub jac.pbs

For more information on PBS, please see the PBS page.