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AMBER

AMBER is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on bio molecules.

AMBER is available as a module on Apocrita.

Usage

To run the latest installed version of AMBER, simply load the amber module:

$ module load amber
$ pmemd --help

  usage: pmemd  [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
              [-ref refc -x mdcrd -v mdvel -frc mdfrc
               -e mden -inf mdinfo -l logfile]
              [-amd amdlog_name -gamd gamdlog_name -scaledMD scaledMDlog_name
               -suffix output_files_suffix]

or for using AMBER with parallel support use:

Parallel support

The below command will only run on parallel nodes.

$ module load amber
$ mpirun -np ${NSLOTS} pmemd.MPI --help

  usage: pmemd  [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
              [-ref refc -x mdcrd -v mdvel -frc mdfrc
               -e mden -inf mdinfo -l logfile]
              [-ng numgroups -groupfile groupfile -rem remd_method]
              [-amd amdlog_name -gamd gamdlog_name -scaledMD scaledMDlog_name
               -suffix output_files_suffix]

Example Jobs

Serial job

Here is an example job for AMBER using 1 core with 5G memory.

#!/bin/sh
#$ -cwd
#$ -j y
#$ -l h_vmem=5G
#$ -l h_rt=1:0:0
#$ -N amber_serial_test

module load amber

pmemd -O \
      -i min_wat.in \
      -o output_min_wat.out \
      -p bpti-ff99SBi.prmtop \
      -c bpti-ff99SBi.inpcrd \
      -r output_min_wat.rst \
      -ref bpti-ff99SBi.inpcrd

Parallel job

Here is an example job for AMBER using 48 cores with an infiniband connection across 2 sdv nodes.

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe parallel 48
#$ -l infiniband=sdv-i
#$ -l h_rt=1:0:0
#$ -N amber_parallel_test

module load amber

mpirun -np ${NSLOTS} pmemd.MPI -O \
       -i min_wat.in \
       -o output_min_wat.out \
       -p bpti-ff99SBi.prmtop \
       -c bpti-ff99SBi.inpcrd \
       -r output_min_wat.rst \
       -ref bpti-ff99SBi.inpcrd

References