From: Olve Peersen (
Date: Fri Jul 03 2009 - 01:26:11 CDT

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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

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 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