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NAMD

NAMD is a molecular dynamics (MD) program designed for parallel computation.

Example run scripts

This script requires that ${INPUT_FILE} be specified. The script is written such that only the number of nodes needs to be changed.

Perlmutter GPU

#!/bin/bash
#SBATCH --qos=regular
#SBATCH --time=02:00:00
#SBATCH --nodes=8
#SBATCH --constraint=gpu
#SBATCH --ntasks-per-node=4
#SBATCH --gpus-per-task=1

module load namd
srun namd2 ${INPUT_FILE}
Perlmutter CPU
#!/bin/bash
#SBATCH --qos=regular
#SBATCH --time=02:00:00
#SBATCH --nodes=4
#SBATCH --constraint=cpu
#SBATCH --ntasks-per-node=64
#SBATCH --cpus-per-task=2

# make sure to load CPU version
module load namd/2.15a2-cpu_mpi
srun namd2 ${INPUT_FILE}

Support

Tip

If after the checking the above you believe there is an issue with the NERSC module file a ticket with our help desk