[gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472

[Justin A. Lemkul]

intra\sa175950 wrote:
> Hi all
> 
>  
> 
> For a research project, I need to know how gromacs work/scale 
> (especially gmx 4.0.4) in SGI ALTIX ICE 8200 EX  machine cluster with 
> Intel Quad-Core E5472. I want to simulate a molecular system (with 14 
> amino acid peptide +/- 5000 water molecules) in explicit conditions with 
> PME and 32 – 64 CPU. I need only to have a (rough) estimation (in 
> ns/day). Does somebody have an example?  
> 
>  

There are benchmarks in the Gromacs 4 paper, as well as on the website.  The 
actual performance will depend upon the connections between your nodes (i.e., 
Infiniband is much faster than Gigabit Ethernet) and the parameters you set in 
the .mdp file (dt, cutoff's, fourierspacing, etc.)

-Justin

> 
> Thanks in advance for your help
> 
>  
> 
> Stef
> 
>  
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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