This is a quick introduction to the usage of the free but licensed code "NAMD2" installed on the HPCVL SunFire systems. It is meant as an initial pointer to more detailed information and a Getting Started primer. It does not replace study of the manual or the NAMD2 web page. 

What is NAMD?

Where is the program located?

How do I set up my environment for NAMD2?

How do I run NAMD2?

Where can I get detailed help?
 

What is NAMD?

NAMD is a parallel code for molecular dynamics simulation of large biomolecular systems, developed by the Theoretical Biophysics Group ("TBG") in the Beckman Institute of the University of Illinois . It is file-compatible with AMBER, CHARMM, and X-PLOR. 

Where is the program located?

The binary executable is  /usr/local/namd2/namd2/namd2 for the SunFire Cluster, while some sample data files are available in /usr/local/namd2/example. The directories /usr/local/namd2/vmd and  /usr/local/namd2/vmd_opengl are for VMD, which has not been successfully tested in the SunFire environment.

How do I set up my environment for NAMD2?
In principle, you don't have to change any settings at for the time being.

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How do I run NAMD2?

To run NAMD2 on the SunFire cluster of HPCVL, at least, you need follow the following steps.

First, you need to become a member of the user group "NAMD2" by downloading a copy of the license from the web page Licence for NAMD2, and the statement file, reading the former, signing the latter, and submitting it to us.

Second, read the manual for the NAMD2, if you are not familier with it.

Third, prepare the input data files. NAMD reads several different input data files formats, which are described in detail in the above manual. You can use/usr/local/namd2/namd2/psfgen to prepare the files. 

Fourthly, it should now be ready for the product calculation. Bear in mind that according to HPCVL policy, users may only submit production calculation jobs via GridEngine. For this, you need a customized version of this script file, modified from the example script file. Simply substitute in values for the four items  between "<" and  ">" and deleting  the "<" and ">" symbols.

There are some tools for further post calculation (visual) analysis (VMD for example). Keep in mind that the SunFire Cluster is primarily for production work and is not for interactive visual analyzing work. HPCVL suggests users download these tools and use them at their own machines. VMD has yet to be tested with the SunFires. VMD will be tested only upon users request.
 
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Where can I get more detailed information?

If you are a new user of NAMD, you should read the manual  and the NAMD2 web page.
These contain useful and important information regarding its use. The examples are also very useful.
Please contact HPCVL Scientific Computing Specialist Gang Liu if you have any questions as he has done some testing with namd2 code.