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How to use 

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How to use How to use

To use this version of Amber set the environment

$ module load amber/20

To understand more about modules see our software applications guide.

Amber 20 supports both serial and parallel versions of the programs. Parallel versions have .MPI suffix, for example, pmemd.MPI, sander.MPI, sandel.LES.MPI. Serial versions of these programs are pmemd, sander, sander.OMP (to run sunder in parallel inside one node) and sander.LES.

Amber pmemd program can also use GPUs. Corresponding executables are pmemd.cuda, pmemd.cuda_DFDP, pmemd.cuda_SPFP,  pmemd.cuda_DFDP.MPI, pmemd.cuda_SPFP.MPI. Indecies DFDP and SFDP stands for double and single precision floating points revisions.

The parallel codes must be executed via an mpirun command.

The serial analysis programs and nmode simulation program should only be submitted with a request for 1 cpu.

Here is a sample job script bench.dhfr for sander from the directory $AMBERHOME/benchmarks/dhfr using project a99 with 10 minutes walltime and 800 MiB memory over 4 CPUs.

#!/bin/bash
 
#PBS -l walltime=10:00
#PBS -l mem=800mb
#PBS -l ncpus=4
#PBS -l software=amber
#PBS -l wd
 
# Load module, always specify version number.
module load amber/20
 
# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`
 
cat <<eof >mdin
  equilbrate apo-dhfr
 &cntrl
    ntb=1, ntp=0,
    ntpr=100,
    ntc=2,  ntf=2, tol=0.000001,
    nstlim=100,
    ntt=0, dt=0.001, ntx=7, irest=1, vlimit=10.0,
 /
eof
 
mpirun sander.MPI -O -i mdin -c md12.x -o bench.dhfr.out

Submit to queueing system:

$ qsub ./bench.dhfr

Using the GPU queue 

#!/bin/bash
 
#PBS -q gpuvolta
#PBS -l walltime=10:00
#PBS -l mem=800mb
#PBS -l ncpus=12
#PBS -l ngpus=1
#PBS -l software=amber
#PBS -l wd
 
# Load modules, always specify version number.
module load cuda/10.1
module load amber/20
 
# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`
 
mpirun -np $PBS_NGPUS pmemd.cuda.MPI -O -i mdin -o mdout -inf mdinfo -x mdcrd -r restrt

Licence requirements

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License requirements License requirements

AmberTools

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public licence (GPL). A few components are included that are in the public domain or which have other, open-source, licences. The sander program now has the LGPL licence.

Amber20

Access to this version of amber is available to users from non-profit organizations (including CSIRO). Commercial use of amber will require prior discussion with the National Facility and have a separate licence arrangement with the Regents of the University of California.

Please note that the software should be referenced in publications.

Please request to join software group on https://my.nci.org.au if you wish to request access.

Authors: Mohsin Ali, Yue Sun, Andrey BLiznyuk