[edit] Amber on the ITS HPC Cluster

Amber (Assisted Model Building with Energy Refinement) contains several molecular simulation programs for molecular mechanics-Poisson Boltzmann/surface area, chemical Monte Carlo/molecular dynamics, protein structure refinement by locally enhanced sampling methodology, NMR refinement, and enzymatic mechanism modeling. It performs well as black-box software for structure-based ligand design. Version 8.0 of Amber is available on the cluster.

The root of the Amber directory tree is /usr/local/amber8/.

To use Amber, load the amber module

   module load amber

A general purpose batch script for sander and pmemd on the ITS Cluster is shown below

# The following script is based on the production.pbs script for the OSC Pentium 4 Cluster
# http://www.osc.edu/hpc/software/docs/amber_oscbw.batch
# AMBER Example Parallel Batch Script for sander or pmemd on the Case ITS HPC Cluster.
# The script runs a job using sander on both processors of 4 nodes with a 24 hr 20 min time limit
#
#PBS -N name_of_job
#PBS -j oe 
#PBS -m ae
#PBS -M your_email_address
#PBS -l walltime=24:20:00
#PBS -l nodes=4:ppn=2
#PBS -S /bin/csh
set echo
module load amber
#
# The path below may need to be changed
set WORK=$HOME/path_of_your_amber_input_files
cd $TMPDIR
#
# The file names below may need to be changed
set MDIN=mdin
set MDOUT=mdout
set MDINFO=mdinfo
set PRMTOP=prmtop
set INPCRD=inpcrd
set REFC=refc
set MDCRD=mdcrd
set MDVEL=mdvel
set MDEN=mden
set RESTRT=restrt
cp $WORK/$MDIN .
cp $WORK/$PRMTOP .
cp $WORK/$INPCRD .
cp $WORK/$REFC .
cp $WORK/$RESTRT .
#
# Periodic, explicit solvent simulations using the paricle-mesh Ewald (PME)
# method may perform better using the pmemd program; change sander to pmemd see manual for more details.
mpiexec sander -O -i $MDIN -o $MDOUT -inf $MDINFO -p $PRMTOP -c $INPCRD -ref $REFC -x $MDCRD -v $MDVEL -e $MDEN -r $RESTRT
ls -al
cp $MDOUT $MDINFO $MDCRD $MDVEL $MDEN $RESTRT $WORK

The most recent version of the sander and pmemd batch script will soon be available in /usr/local/amber8/current/production.pbs. Users should edit their copy of this script appropriately. On the cluster this script executes sander in parallel; sander scales reasonably up to 16 processors (8 nodes, 2 processors per node).

Information on submitting batch scripts to the cluster is available in the ITS HPC cluster "quick start" document (requires Case IP address and cluster account ID and password)

It is important that batch scripts be in the Unix text file format. The procedure to convert Windows text file to the Unix text file format is covered in ITS HPC cluster FAQ

Input files for the examples in the manual are available in the examples subdirectory. Other examples are also available in the test and benchmarks subdirectories.

Several tutorials are available at the Amber Tutorials page

General documentation is available from the Amber home page.

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