NAMD
Last Modified: 05/01 9:24
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
- 2.6, 2.7b1
Authorized Users
- circe account holders
Platforms
- circe cluster
Local Documentation
Modules
Namd requires the following module file to run:
- apps/namd/2.6 or apps/namd/2.7b1
See Modules for more information.
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 following job script will run NAMD over eight processors on InfiniBand with an 8 hour CPU time limit:
#$ -N namd_job #$ -j y #$ -o output.$JOB_ID #$ -cwd #$ -pe ompi* 8 #$ -l h_cpu=08:00:00,i_ib=true module add apps/namd/2.7b1 sge_mpirun namd-2.7b1 *.conf
Benchmarks & Tutorials
The above User Information & Documentation links should have ample information to qualify as a tutorial. We currently have one benchmark in the directory
- /opt/apps/namd2/apoa1
This is a fairly standard NAMD benchmark that is used for testing clusters.
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs directly to Research Computing: mailto:support@rc.usf.edu
