Re: need advices for running NAMD efficiently.

From: Axel Kohlmeyer (
Date: Mon Jun 15 2009 - 13:19:05 CDT

On Mon, 2009-06-15 at 10:44 -0700, Lixia Jin Day wrote:
> Dear all,
> We recently switched to our project to another computer cluster, which
> we have to pay 2.5 cents for every CPU time. As our system is huge,
> over 350,000 atoms, I need to find a better way to run our simulation.
> Please give some of your advices. Thank you!

dear lixia,

two suggestions:

1) have a close look at the NamdWiki. there are many useful suggestions
   to optimize your parameters.

2) make some benchmark tests and test for maximum scaling and maximum
   throughput. those are usually not the same and you can make a choice
   as to how much money it is worth to you to get your results quickly.


p.s.: computer time on teragrid "only" costs writing a
proposal currently.

> Best,
> Lixia

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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