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Information

Purpose: Molecular Dynamics
Latest version: 2.12
License: Mixed - Free for non-commercial users
Website: http://www.ks.uiuc.edu/Research/namd/

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.).

 

 

Benchmark

NAMD 2.11 benchmark at Collserola

Actual speed-up (green) and ideal speed-up (blue) vs. number of cores for the standard NAMD benchmark, ApoA1.

Please note that employing the Xeon Phi coprocessor for offload acceleration provides 1-3x speed-up when compared with CPU-only runs.

 

 

SLURM Submit script example

For more information use the Job Script Generator.

adf_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=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G

module load apps/namd/2.12

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

cd $TMPDIR
cp -r $INPUT_DIR $TMPDIR
namd2 +p4 namd_example.namd > namd_example.out
cp ./* $OUTPUT_DIR

 

 

 

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