Amber/AmberTools

Amber and AmberTools are suite of biomolecular simulation programs. Here, the term “Amber” does not refer to the set of molecular mechanical force fields for the simulation of biomolecules but to the package of molecular simulation programs consisting of the AmberTools (sander and many more) and Amber (pmemd).

AmberTools are open-source while Amber (pmemd) requires a license. FAU holds a license for non-commercial academic use through the Department of Biochemistry. Contact hpc-support@fau.de for activation of the amber module.

Availability / Target HPC systems

  • TinyGPU: only pmemd.cuda – but best performance if input is supported by pmemd.
    Only a single GPU can be used  by pmemd.cuda.
  • throughput cluster Woody and parallel computers: only use sander.MPI if the input is not supported by pmemd.MPI.
    cpptraj is also available in parallel versions (cpptraj.OMP and cpptraj.MPI).

New versions of Amber/AmberTools are installed by RRZE upon request.

Notes

The CPU-only module is called amber while the GPU version (which only contains pmemd.cuda) is called amber-gpu. The numbers in the module name specify the Amber version, Amber patch level, the AmberTools version, and the AmberTools patch level. The number are complemented by the used compilers/tools, e.g. amber/18p14-at19p03-intel17.0-intelmpi2017 or amber-gpu/18p14-at19p03-gnu-cuda10.0.

pmemd and sander do not have internal measures to limit the run time. Thus, you have to estimate the number of time steps which can finish within the requested wall time before hand and use that in your mdin file.

Recent versions of AmberTools install their only version  of Python which is independent of the Python of the Linux distribution or the usual Python modules of RRZE.

Sample job scripts

#!/bin/bash -l
#PBS -lnodes=1:ppn=4,walltime=10:00:00
#PBS -N my-pmemd
#PBS -j eo

cd $PBS_O_WORKDIR

module add amber-gpu/18p14-at19p03-gnu-cuda10.0

### there is no need to fiddle around with CUDA_VISIBLE_DEVICES!

pmemd.cuda -O -i mdin ...

#!/bin/bash -l
#PBS -lnodes=4:ppn=40,walltime=10:00:00
#PBS -N my-pmemd
#PBS -j eo

cd $PBS_O_WORKDIR

module add amber/18p14-at19p03-intel17.0-intelmpi2017

mpirun -pinexpr S0:0-9@S1:0-9 pmemd.MPI -O -i mdin ...

Further information

Mentors

  • Dr. A. Kahler, RRZE, hpc-support@fau.de
  • AG Sticht (Professur für Bioinformatik, MedFak)