AMBER

The Assisted Model Building with Energy Refinement (AMBER) package contains many molecular simulation programs targeted at biomolecular systems. A wide variety of modelling techniques are available. It generally scales well on modest numbers of processors, and the GPU enabled programs are very efficient.

Availability & Restrictions

Amber is available to all OSC users once they have completed a copy of the Academic Agreement form

Version Glenn Oakley
9 X  
10 X  
11 X X
12 X X

Usage

Set-up

Initalizing Amber on both Glenn and Oakley is done by loading an amber module:

module load amber

To see other available versions, run the following command:

module avail

Using AMBER

To execute a serial Amber program interactively, simply run it on the command line, e.g.:

tleap

Parallel Amber programs should be run in a batch environment with mpiexec, e.g.:

mpiexec pmemd.MPI

Batch Usage

Sample batch scripts and Amber input files are available here:

/nfs/10/srb/workshops/compchem/amber/

This simple batch script for either Glenn or Oakley demonstrates some important points:

# AMBER Example Batch Script for the Basic Tutorial in the Amber manual
#PBS -N 6pti
#PBS -l nodes=1:ppn=1
#PBS -l walltime=0:20:00

module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp -p $PBS_O_WORKDIR/6pti.prmtop .
cp -p $PBS_O_WORKDIR/6pti.prmcrd .
# Running minimization for BPTI
cat << eof > min.in
# 200 steps of minimization, generalized Born solvent model
&cntrl
maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
/
eof
sander -i min.in -o 6pti.min1.out -p 6pti.prmtop -c 6pti.prmcrd -r 6pti.min1.xyz
cp -p min.in 6pti.min1.out 6pti.min1.xyz $PBS_O_WORKDIR

Further Reading

 

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