NAMD is an application for high-performance, parallel, scalable molecular dynamics simulations. NAMD scales to hundreds of processors on high-end parallel platforms. It uses the molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.
 
Usage
A fully parallelized version of NAMD is available on the Bioinformatics cluster. It takes advantage of the cluster's 64-CPU architecture for high-performance molecular dynamics simulations. To get an account on the cluster please see the Accounts page or contact Richard Casey below.
 
On the cluster, the NAMD shell script

"namd.sh"

is available in the directory

"/common/namd"

You may copy this file to your home directory (or other locations) to run NAMD.

Submit "namd.sh" to the batch queues on Bioinformatics cluster:

"qsub namd.sh"

Enter the command "qstat" to follow the progress of your batch job.

When the batch job is finished, results files will be sent to your home directory (or other directories as specified in the shell script).

NAMD documentation (below) describes in detail how to use all the capabilities of the application. The namd.sh shell script can be modified accordingly to take advantage of these features.
 
Documents
Documentation for NAMD is available in the documents webpage.
 
NAMD Website
For more information about NAMD, visit the NAMD website
 
For more information contact:
Richard Casey, PhD
Ph: 970-491-8568
Cell: 970-980-5975
Email: richard.casey@colostate.edu
 

© Copyright 2008, Colorado State University
Fort Collins, Colorado 80523
Maintained by Richard Casey