NAMD

Description

From the NAMD manual: NAMD (NAnoscale Molecular Dynamics) can simulate the movement of proteins with millions of atoms, making it the world’s fastest parallel molecular dynamics program. The NAMD development team will continue to incorporate the latest parallel-computing advances into NAMD, which already runs efficiently on several thousand parallel processors.

Version

2.12

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

NAMD requires the following module file to run:

apps/namd/2.12

See Modules for more information.

Running NAMD on CIRCE/SC

The NAMD user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

NAMD can run well on most types of hardware on the cluster. For the vast majority of cases, memory is not as big an issue as CPU time and the program is parallel “enough” to ensure that it runs reasonably well over GigE though it will run better on Myrinet or InfiniBand.

The script below (for testing, name it “namd-test.sh”) can be copied into your job directory (the folder with your input .conf files) and modified so that you can submit batch processes to the queue.

NOTE: If you have more than one .conf file in this directory, it will process them all.

#!/bin/bash
#
#SBATCH --comment=namd-test
#SBATCH --ntasks=8
#SBATCH --mem-per-cpu=1024
#SBATCH --job-name=namd-test
#SBATCH --output=output.%j.namd-test
#SBATCH --time=01:00:00

#### SLURM 8 processor NAMD test to run for 1 hour using 8 GB of memory.

module purge
module add apps/namd/2.12

mpirun namd2 *.namd

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./namd-test.sh

You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

NAMD Home Page
- http://www.ks.uiuc.edu/Research/namd/
NAMD User's Guide
- http://www.ks.uiuc.edu/Research/namd/2.12/ug/

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

NAMD Benchmarks
- /apps/namd/examples/

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with NAMD to the IT Help Desk: rc-help@usf.edu