NAMD - Scalable Molecular Dynamics

Motivation

The NAMD molecular parallel molecular cynamics package is supported from the University of Illinois NCSA as part of the NIH bioinformatics software effort. It scales to use some dozens of processors using gigabit ethernet. It uses VMD for simulation setup, but is also file-compatible with AMBER, CHARMM and X-PLOR.

Using NAMD

After logging into login01 or login02, e.g. by:

ssh -l myunityid login.hpc.ncsu.edu 

Type:

add namd

at the command line. If the file bnamd2 is in the same directory as the input file ubq_wb_eq.conf, then executing the command:

bsub < bnamd2 

will execute NAMD. The file bnamd2 is as follows:

#!/bin/csh
#BSUB -o o.%J
#BSUB -W 15
#BSUB -n 4
#BSUB -R xeon
mpiexec /usr/local/apps/NAMD2.6/linux86/Linux-i686-MPI/namd2 ubq_wb_eq.conf > ubq_ws_eq.log 

The flag "-W 15" requests at most 15 minutes. The flag "-n 4" requests 4 processors. Asking for at most 15 minutes and 4 processors puts the job in debug mode, so that you can quickly correct mistakes and resubmit. Once you're sure a job will start, then you can ask for more processors and time, but in that case, your job will likely wait in queue. The flag #BSUB -R xeon specifies that the code will run on a 32 bit blade.

Links to Tutorial and Documentation

For some tutorials and example codes for using NAMD, see NAMD tutorial and NAMD home page.