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.
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
|Module||Version||Module Load Command|
|namd||2.14||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.