Prem's den

What is NAMD ?

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is our hope that this project serves as an inspiration for other Grid users to bring their projects to the grid.

How to compile NAMD ?

You don't have to worry about it as the application binary is already available on the Sungrid compute utility. All you have to do is , check-out NAMD from the application catalog, create a data resource and run NAMD ! If you insist on compiling it or you need assistance in compiling NAMD on a solaris box, jeevan's blog can help you out.

How to run NAMD on Sungrid ?

If you are familiar with the sungrid, here is what is take to run the app on sungrid.

• > Place all the input data files in a directory named "data". A sample can be found here .
  
• > Mention the number of slots you would like to run namd on in the data/slots.in file.
• > Zip the data directory and upload it as NAMD_data resource.
• > Checkout NAMD from the Application Catalog.
  
• > In the jobs tab, edit the NAMD catalog job and point the NAMD_data resource to the newly created namd resource. 
• > Run the job and download the output.

Sample Run :

• > Download the NAMD sample data resource from here
• > Create a Data Resource with the downloaded zip file.
• > Checkout NAMD from the Application Catalog.
• > In the Jobs Tab, edit the NAMD Job and point the "NAMD_data" resource to the one created above.
• > Save and Run the Job.

For more on information see here. A sample input visualized through VMD and the expected result of the test run are posted in the link provided. Please share you experiences in runnng the application and help me improve the usability.