Purpose: Molecular Dynamics
Latest version: 20
Licence: (warning) Must be provided by the user.
                 Proprietary licence ext-link
Website: http://ambermd.org/_ext-link

Amber is a collection of programs for setting-up, running and analysing molecular dynamics simulations.

Amber refers both to a collection of about 50 programs for building, configuring and minimising molecular structures, setting up force fields, running simulations, analysing trajectories, and computing system properties, and to a force field for biomolecules implemented by the Amber programs.

SLURM Submit script example

More information about the submit script can be found using the Job Script Generator.


#!/bin/bash
#SBATCH -J amber_example
#SBATCH -e amber_example.%j.err
#SBATCH -o amber_example.%j.out
#SBATCH -p std
#SBATCH -n 1
#SBATCH -t 0-02:00

module load apps/amber/18

##
#  Modify the input and output files!

cp -r ${SLURM_SUBMIT_DIR}/{*.inp,*.top,*.crd} ${SCRATCH}
cd ${SCRATCH}
 
srun pmemd.MPI -O \
               -i amber_example.inp \
               -p amber_example.top \
               -c amber_example.crd \
               -o amber_example.out
 
cp ./*.out ${SLURM_SUBMIT_DIR}

Sbatch options:

The options shown in the example are detailed below. For more information and a more comprehensive list of available options, see the sbatch command page.

  • -J: Name for the job's allocation.
  • -e: Name of the sterr redirection filename.
  • -o: Name of the stdout redirection filename.
  • -p: Name of the partition (queue) where the job will be submited.

  • -n: Number of tasks.

  • -t: Set the job's time limit. If the job don't finish before the time runs out, it will be killed.

Software execution information:

The pmemd program is the comercial-high-performance version of sander, general purpose MD engine of Amber. Here is a summary of the command line options for them:

  • -O: Overwrite output files if they exist.
  • -A: Append output files if they exist.
  • -i: Input file. Default input name: mdin.
    • Contains control data for the min/md run.
  • -p: Input file. Default input name: prmtop.
    • Contains molecular topology, force field, periodic box type, atom and residue names.
  • -c: Input file. Default input name: inpcrd.
    • Contains initial coordinates and (optionally) velocities and periodic box size.
  • -r: Output structure file. Default input name: restrt.
    • Contains final coordinates, velocity, and box dimensions for restarting run.
  • -o: Output energy file. Default input name: mdout.
    • Contains user readable state info and diagnostics.
    • -o stdout will send output to stdout (to the terminal) instead of to a file.
  • -x: Output energy file. Default input name: mdcrd.
    • Contains coordinate sets saved over trajectory.
  • -e: Output energy file. Default input name: mden.
    • Contains extensive energy data over trajectory (not synchronized with mdcrd or mdvel).
  • -inf: Output energy file. Default input name: mdinfo.
    • Latest mdout-format energy info.