NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of cores for typical simulations, however NAMD calculations are restricted to at most a single node on the JADE service.

Job scripts

Below is an example of a NAMD job script


#SBATCH --nodes=1
#SBATCH --ntassk-per-node=20
#SBATCH --job-name=testNAMD
#SBATCH --time=01:00:00
#SBATCH --gres=gpu:4

module load NAMD/2.12

$NAMDROOT/namd2 +p$SLURM_NTASKS_PER_NODE +setcpuaffinity +devices $CUDA_VISIBLE_DEVICES ./input.conf &> run.log

The above example utilises half the resources on a JADE node, with a requests for a single node with 20 tasks and 4 GPUs.

Because the job is run on a single node, NAMD can be started directly, thus avoiding the use of the launcher charmrun. The application is set to run on the resources allocated uwing the +p and +devices command line options. Additionally, affinity is requested using the option +setcpuaffinity.

The general recommendation is to have no more than one process per GPU in the multi-node run, allowing the full utilisation of multiple cores via multi-threading. For single node jobs, the use of multiple GPUs per process is permitted.

To read more about NAMD processing on GPUs, please visit .

Installation notes

The latest version of the source code was used and built using OpenMPI v1.10.5a1 and GCC v4.8.4 following instructions from

Charm++ was built using:

./build charm++ verbs-linux-x86_64 gcc smp --with-production

NAMD was built using the following:

./config Linux-x86_64-g++ --charm-arch verbs-linux-x86_64-smp-gcc --with-cuda --cuda-prefix /usr/local/cuda-8.0

For the decision on the number of threads to use per node, take a look at