Amber

Molecular dynamics

Description

Amber is a molecular dynamics package which has as number of additional tools for more sophisticated analysis and in particular for NMR structure refinement.

Amber10 has been installed on Vuori. The other servers don't yet have an official installation. To start using it give

module load amber (or amber/10)

This will set $AMBERHOME and put the binaries in the path. To run a serial sander job in the batch queue give

Examples for batch jobs

You can find example inputs from the amber tests directory:

ls $AMBERHOME/test

In Vuori a serial sander batch job

#!/bin/csh
#SBATCH -p serial
#SBATCH -n 1
#SBATCH -t 16:00:00
#SBATCH -J testing
#SBATCH --mail-type=END
#SBATCH --mail-user=your.username@in.there

setenv MV2_ENABLE_AFFINITY 0
module load amber

srun sander -O -i mdin -c gcg.x -o gcg.out

Submit the job with

sbatch your.script

A parallel sander job in Vuori (note the partition name=serial up to 12 cores!):

#!/bin/csh
#SBATCH -p serial
#SBATCH -n 12
#SBATCH -t 16:00:00
#SBATCH -J testing
#SBATCH --mail-type=END
#SBATCH --mail-user=your.username@in.there

setenv MV2_ENABLE_AFFINITY 0
module load amber

srun sander.MPI -O -i mdin -c gcg.x -o gcg.out

In vuori a parallel pmemd job (note partition name=parallel when it's bigger than 12!):

#!/bin/csh
#SBATCH -p parallel
#SBATCH -n 24
#SBATCH -t 16:00:00
#SBATCH -J testing
#SBATCH --mail-type=END
#SBATCH --mail-user=your.username@in.there

setenv MV2_ENABLE_AFFINITY 0
module load amber

srun pmemd -O -i mdin -o mdout -p prmtop -c inpcrd

The pmemd module scales up to some tens of cores in Vuori, but is much slower than e.q. Gromacs. For large scale or very long MD simulations consider using a better tuned MD engine.

Example for a serial interactive job

Sometimes it is more convenient to run a small job, like system preparations, interactively. To prevent load on the login node, these can be run on the compute nodes. For example, the above serial job:

salloc -n 1 srun sander -O -i mdin -c gcg.x -o gcg.out

or to test the input of a pmemd run:

salloc -n 4 srun pmemd -O -i mdin -o mdout -p prmtop -c inpcrd

More information

Amber home page: http://ambermd.org/

If you have questions on running Amber at CSC, contact helpdesk (at) csc.fi or Atte.