Help building a desktop for namd

From: Salvador H-V (
Date: Sun Apr 10 2011 - 12:40:05 CDT

Hi all,

I am new to the biomolecular world of computer simulations. I would like to
learn from scratch how to use namd.
I am thinking to build a basic desktop computer to run the tutorials and
some simulations.

At this moment, I think that phenom II x6 1000T amd (six-core) processors
are my best option (economic reasons). However, I was wondering if you could
share some of your expecience using namd and vmd with amd processors.
Besides, I am also worried about the performance of amd processors with free
intel compilers. I know that free intel compilers perform very well on I7,i6
& i3 but what about namd proccesors, any idea about this issue?

Finally, I am thinking to use the six-core amd proccesors togehter with a
GeForce GTX 580, to be able to use CUDA with namd and vmd, there is
something that I should be aware of such combination?

Any help or suggestion would be greatly appreciated.

Thanks a lot,

Salvador HV

P.S I will use at least 8gb in ram

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