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Information

Purpose: Molecular Dynamics
Latest version: 14
Licence: Proprietary licence
Website: http://ambermd.org/ extlink-icon

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 information 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
#SBATCH --mem=4G

module load apps/amber/14

INPUT_DIR=${PWD}
OUTPUT_DIR=${PWD}

cd $TMPDIR
cp -r $INPUT_DIR $TMPDIR
mpijob amber_example.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.

 

 

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