Amber

Introduction

Before you are able to access AMBER, you will be asked to read and agree to the licence terms.

These can be viewed by following this link. You are recommended to print out and sign a copy for your own reference.

To access Amber, load its module through:

$ module load amber

This sets the AMBERHOME environment variable and your path to include the bin directory, with common executables as follows:

$AMBERHOME/bin/sander # Serial version of SANDER

$AMBERHOME/bin/sander.MPI   # built to run over Infiniband

$AMBERHOME/bin/pmemd  # Serial version of PMEMD

$AMBERHOME/bin/pmemd.MPI   # pmemd built to run over Infiniband

Example job submission scripts

The following script will run pmemd on 16 cores for 48 hours, the module command is included in the submission script therefore it is not necessary to have the environment loaded prior to job submission:

#!/bin/sh
#$ -cwd
#$ -l h_rt=48:00:00
#$ -pe ib 16
module add amber

l=md19
f=md20
mpirun pmemd.MPI  -O -i $f.in -o $f.out -inf $f.inf \
        -c gc90turn10wat.$l -ref gc90turn10wat.$l -r gc90turn10wat.$f \
        -p gc90turn10wat.top -x gc90turn10wat$f.x -e gc90turn10wat$f.ene

This script can be submitted to the batch queues with:

$ qsub run.sh