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Information

Purpose: Molecular Dynamics
Latest version: 18
Licence: Proprietary licence
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

For more configuration options use the Job Script Generator.

amber_example.slm
#!/bin/bash
#SBATCH -J amber_example
#SBATCH -e amber_example.err
#SBATCH -o amber_example.out
#SBATCH -p std
#SBATCH --nodes=1
#SBATCH --ntasks=1

module load apps/amber/14

INPUT_DIR=${SLURM_SUBMIT_DIR}
OUTPUT_DIR=${SLURM_SUBMIT_DIR}

cd $SCRATCH
cp -r $INPUT_DIR/* $SCRATCH
mpirun -np $SLURM_NTASKS pmemd.MPI -O \
 -i amber_example.inp \
 -p amber_example.top \
 -c amber_example.crd \
 -o amber_example.out
cp ./* $OUTPUT_DIR

Sbatch options:

  • -J: Specify a name for the job allocation. The default is the name of the batch script.
  • -e: Specify a name for the error output file.
  • -o: Specify a name for the output file.
  • -p: Specify the name of the partition (queue) where the job will be submited. The default is std.
  • --nodes: Number of nodes requested for allocation.
  • --ntasks: Number of processes requested for allocation.
  • --mem-per-cpu: Memory allocated per core.

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.



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