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 firstname.lastname@example.org 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:
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:
A serial Amber program in a short duration run can be executed interactively on the command line, e.g.:
Parallel Amber programs must be run in a batch environment with mpiexec, e.g.:
The CUDA Amber programs, which must be run in a batch environment, are recommended due to thier computational performance; e.g.:
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.
Sample batch scripts and Amber input files are available here:
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