how best to build a GPU-accelerated desktop machine for NAMD?

From: Erik Nordgren (
Date: Fri Nov 19 2010 - 20:08:48 CST

Hello all,

I've spent some time searching through the forums here, and looked elsewhere
online as well, in the hopes that my question (below) would already have
been answered explicitly, but haven't found what I'm seeking, so...

My question is this: if one were to put together a new desktop machine
today, in order to get impressive performance for CUDA-enabled NAMD, what
exactly would one need?

I do realize this is a rather open-ended question, and I don't expect
someone to hand me a precise shopping list per se; but what would be really
nice would be some general guidance. Perhaps it would be better to break
this down into a few more questions:

1) are NVIDIA GPUs the only option for CUDA performance gains, or are other
brands now worth considering?
2) what are the most important GPU parameters... e.g., RAM capacity, #cores,
clock rate, something else?
3) are there, in fact, specific GPU models that are for some reason highly
4) how important (if at all) would be the speed and/or number of *CPUs* (or
cores) in such a machine?
5) could one expect to get correspondingly-better NAMD performance from
multiple *GPUs* in one machine?
6) how much system RAM would be needed?
7) are there any other system components (e.g., 64-bit OS, motherboard,
other hardware) that could have a significant performance impact?

Just a couple more ballpark parameters for my specific situation:
- the simulations I would envision running would involve perhaps 50,000 to
150,000 atoms, including a fair amount of explicit solvent
- my budget for the machine would be something in the neighborhood of $1500
to $3000 (depending on relative bang-for-the-buck)

thanks for reading, and thanks all the more for any helpful replies!
- Erik

C. Erik Nordgren, Ph.D.
Chemistry Department
University of Pennsylvania

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