Amber/PMEMD

Useful links

Licensing and Access

Amber is licensed software. Please see the Amber web page for details. Users who wish to access the Amber package should submit a request via SAFE.

Running

To run Amber or PMEMD you need to add the correct module.

module add amber

will give you access to Amber.

Running Amber

An example sander job submission script is shown below.

#!/bin/bash --login
#PBS -N sander_job
#PBS -l select=4
#PBS -l walltime=00:30:00
# Replace this with your budget code
#PBS -A budget

# Move to directory that script was submitted from
export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
cd $PBS_O_WORKDIR

module load amber

export MPICH_FAST_MEMCPY=1
export MPI_COLL_OPT_ON=1

# Set the number of threads to 1
#   This prevents any system libraries from automatically 
#   using threading.
export OMP_NUM_THREADS=1

# please change the options of sander according to your needs
date
aprun -n 96 sander.MPI -O -o results.out
date

Running PMEMD

An example PMEMD job submission script is shown below.

#!/bin/bash --login
#PBS -N pmemd_job
#PBS -l select=64
#PBS -l walltime=00:30:00
# Replace this with your budget code
#PBS -A budget

cd $PBS_O_WORKDIR

module load amber

export MPICH_FAST_MEMCPY=1
export MPI_COLL_OPT_ON=1
# please change the options of pmemd according to your needs
date
aprun -n 1536 pmemd.MPI -O -o results.out
date 

Compiling