Re: Help building a desktop for namd

From: Salvador H-V (
Date: Mon Apr 11 2011 - 12:22:01 CDT

Hi Axel,

Thanks for your reply and suggestions.

In your reply you mentioned that: "as i said before, any serious
calculation will have to be run on a serious machine anyways, so building a
desktop for that is a waste of energy and money. "

Because I don`t have any experience in supercomputing, I would like to ask
you some questions about building a desktop or small cluster for
bio-molecular simulations.

i) It is not possible at all running some decent systems in a desktop?. In
other words, what are the minimal requirements for a desktop or server to
run some serious calculations?

ii) I though that using a good processor and plenty of memory ram with a
good GPUs could be the job, but it seems that I am completely wrong. So, I
was wondering what percentage of namd capabilities could be exploited using
only GPUs?

iii) I will receive some small funding from government and I would like to
buy or built some computers to run biomolecular simulations. To be sincere,
we don`t have the experience neither the money to built a standard cluster
of hundred of processors. In fact, we are looking for the minimum cluster
requirements that can run NAMD (with GPUs) for relative small systems (~
40000-100 000 atoms). Any suggestion about what is the best way to proceed?

If the funding is approved we will have to built by our own a small cluster.
There is not many people with expertise around that can help us. Any
suggestion, help or information would be greatly appreciated.

Thanks a lot,


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