Description

NAMD is a parallel molecular dynamics code designed for high-performance simulation of
large biomolecular systems.


Software Category: chem

For detailed information, visit the NAMD
website.

Available Versions

The current installation of NAMD
incorporates the most popular packages. To find the available versions and learn how to load them, run:

module spider namd

The output of the command shows the available NAMD
module versions.

For detailed information about a particular NAMD
module, including how to load the module, run the module spider command with the module’s full version label. For example:

module spider namd/2.14

NAMD with MPI

The NAMD module was built on the HPC system with MPI support. Below is a Slurm script template.

#!/bin/bash
#SBATCH -A mygroup             # your allocation account
#SBATCH -p parallel            # partition
#SBATCH -N 2                   # number of nodes
#SBATCH --ntasks-per-node=40   # number of tasks
#SBATCH -t 24:00:00            # time

module purge
module load goolf namd
mpiexec namd2 input.namd       # please use mpiexec as the executor for NAMD

You may want to benchmark it to see how well it scales for the type of job that you are running. Please refer to our tutorial on this topic.