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 CUDA programs are very efficient.

Availability & Restrictions

Amber is available to not-for-profit OSC users; simply contact oschelp@osc.edu to request access.  For-profit OSC users must obtain thier own Amber license.  These versions are available, where S means serial executables, P means parallel, and C means CUDA:

Version Glenn Oakley
9 SP  
10 SP  
11 SPC SPC
12 SPC SPC
14 SP SPC

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

A serial Amber program in a short duration run can be executed interactively on the command line, e.g.:

tleap

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

mpiexec pmemd.MPI

The CUDA Amber programs, which must be run in a batch environment, are recommended due to thier computational performance; e.g.:

pmemd.cuda

For supported features of the GPU accelerated version of PMEMD see Amber GPU Support.

In Amber14 intra-node multi-GPU pmemd.cuda.MPI jobs are not yet supported on Oakley.

In Amber14 the CUDA programs no longer support Glenn's hardware, and thus cannot be installed.

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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