Re: vmd-l: Hardware for NAMD / VMD machine

From: John Stone (
Date: Mon Jul 06 2009 - 11:04:30 CDT

  Axel's suggestions are good. The main comment I have is
that the primary benefit of the Quadro GPUs is larger memory
capacity and support for stereoscopic rendering. If you need
support for quad buffered stereoscopic rendering, then there's
not presently much of an alternative to the Quadro cards.
If you just need the large memory capacity in order to use CUDA
for electrostatics calculations or the like, then a less costly
alternative is to buy a Tesla C1060. If you don't need either of
these features, then the consumer video game GPUs such as the
GeForce GTX 285 may work fine for you.

You should consider whether you'll be using the GPUs for
long-running CUDA calculations as well, e.g. NAMD, and
if so, then getting Tesla C1060s for that purpose would be
advised since they undergo much more reliability testing than
the the consumer video game GPUs do.

  John Stone

On Fri, Jul 03, 2009 at 12:26:11AM -0600, Olve Peersen wrote:
> ========= Note: This message has been sent to both NAMD and VMD
> mailing lists ==============
> We're looking into buying a new Linux box for structural biology
> refinement and some molecular dynamics work (i.e. equilibration runs
> and making sure input files are right before handing jobs off to
> bigger clusters) and I wanting to get some input on where it is worth
> spending money on the system from a NAMD/VMD perspective. Our
> experimental systems are proteins of 150-500 residues in size, and we
> already have some experience running NAMD/VMD on an older Pentium 4D
> system with a Quadro FX1300 and hardware stereo.
> At the moment I am leaning toward a dual Xeon 55XX (quad-core) system
> with 12 GB of RAM - this is the Xeon version of the quad-core Core i7
> Nehalem processor. My choice will probably end up being the midrange
> 5520 or 5530 processors (2.26 vs 2.40 GHz) unless there is a really
> good computational reason to go to the faster X series, where I
> suspect I'll be mostly paying a "bleeding-edge premium".
> For NAMD it seems that more and faster processors, more RAM, and fast
> disks are the key elements. I'm not up for doing full cluster
> architecture, so any inter-machine connections would be gigabit for
> the time being. I also suspect I'd be better off compiling with the
> Intel compilers and certain Xeon specific flags as some processor
> specific tweaking is apparently worthwhile for the new Nehalem
> architecture, but that is something I have not seriously looked into
> yet.
> The question I've had a harder time nailing down is how dependent VMD
> performance is on the graphics card versus the core system itself and
> how powerful a 3D graphics card I should invest in. In our experience
> thus far, rendering of our systems seems fine with our old Quadro
> FX1300 and I was thinking of going with a 768 MB Quadro FX1800 for
> this new system, but I could spend another $400 and get a 1GB FX3800,
> or get really carried away with ~$1700 for a FX4600/4800 card. Is
> there a compelling performance reason for doing so?
> Thanks in advance for any input,
> Olve
> -------------------------------------------------------
> Olve Peersen
> Associate Professor
> Dept. of Biochemistry & Molecular Biology
> 1870 Campus Delivery
> Colorado State University
> Ft. Collins, CO 80523-1870
> -------------------------------------------------------
> 970.491-0433 Office
> 970.491-0271 Lab
> 970.491-0494 Fax
> -------------------------------------------------------

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