Purpose: Molecular Dynamics
Latest version: 20
Licence: Must be provided by the user.
Proprietary licence
Website: http://ambermd.org/
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.