[gmx-users] Gromacs 4.0 Benchmarks

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 11 00:42:39 CET 2009

Robert Fenwick wrote:
> Hi,
> I wanted to run one of the gromacs 4.0 benchmarks on a new cluster
> that we have and also wanted to see the affect of this 4 fs time step.
> If it would not be too much trouble would it be possible for the
> setups of either the PLINCS paper or the GROMACS 4.0 paper to be
> placed somewhere on the website. Specifically I am intersted in the
> lysozyme benchmark, however I suspect others might like the membrane
> system to as well.
> I have tried to set a similar simulation up, but it is not able to run
> with 4 fs integration.

So what exactly is going wrong?  What is in your .mdp file?  It is probably 
better for you to post this information here and receive feedback, so that 
others can make use of it later.

The methodology for the lysozyme benchmark is pretty explicit in the Gromacs 4 
paper; is there some aspect that is not clear?


> Bryn
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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