AMBER

Amber

Versions Installed

Fionn: 11, 12

Description

Amber (Assisted Model Building with Energy Refinement), is a general purpose molecular mechanics/dynamics suite which uses analytic potential energy functions, derived from experimental and ab initio data, to refine macromolecular conformations.

License

ICHEC has acquired a site license for the Amber 11 (AmberTools 1.5) and Amber12 (AmberTools 12) packages.

Benchmarks

The Amber Benchmarks from Mike Wu and Ross Walker were run on the Fionn cluster.

Thin Component

Amber 11 is used in the same way as Amber 12 on Fionn except the appropriate module should be loaded. Assuming that this PBS script is saved as amber.pbs, the job can be submitted to the queue by running the following command in the same directory 

qsub amber.pbs

A job submission example is as follows.

#!/bin/bash
#PBS -l nodes=2:ppn=24
#
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the Amber module
module load molmodel amber/intel/12

cd $PBS_O_WORKDIR

mpiexec $AMBERHOME/exe/pmemd.MPI -O -i mdin -p prmtop -c inpcrd -ref inpcrd -suffix outSuffix

GPU

Job Submission Example on Fionn 1 node with 2 K20 GPUs. This will use as many GPUs as it can find. On one node of Fionn this is 2. Note that the number of MPI processes must be the same or less than the number of GPUs available.

#!/bin/bash
#PBS -l nodes=1:ppn=20
#
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName
#PBS -q GpuQ

#Load the Amber module
module load molmodel amber/intel/12

cd $PBS_O_WORKDIR

export CUDA_VISIBLE_DEVICES=0,1
mpiexec -ppn 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -o mdout.2K20 -inf mdinfo.2K20 -x mdcrd.2K20 -r restrt.2K20 -ref inpcrd

Additional Notes

To use a version of Amber load the relevant environment module:

Fionn

module load molmodel amber/intel/11

module load molmodel amber/intel/12