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Information

Purpose: Molecular Dynamics
Latest version: 2.13
License: Mixed - Free for non-commercial users
Website: http://www.ks.uiuc.edu/Research/namd/ext-link

NAMD is a molecular dynamics package.

NAMD implements standard MD capabilities (variety of integrators, thermostats, barostats, force field compatibility, PME electrostatics, timestep integration, replica exchange, free energy calculations, etc.). 

NAMD is also available to run on GPU NODES showing up to 8X performance (at same number of cores as std nodes). To perform GPU computations, please contact support team. 



SLURM Submit script example

For more information use the Job Script Generator.

namd_example.slm
#!/bin/bash
#SBATCH -J namd_example
#SBATCH -e namd_example.err
#SBATCH -o namd_example.out
#SBATCH -p std
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=4GB


module load apps/namd/2.13

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

cd $SCRATCH
cp -r $INPUT_DIR/* $SCRATCH
mpirun `which namd2` namd_example.namd > namd_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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