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
ModuleVersion Module Load Command
namd2.14 module load gcc/9.2.0 openmpi/3.1.6 namd/2.14

NAMD with MPI

The NAMD module was built on Rivanna 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.