[gmx-users] Re: PME slows down
Jason de Joannis
jdejoan at emory.edu
Thu Jun 2 16:58:06 CEST 2005
> Date: Thu, 02 Jun 2005 10:52:27 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re: PME slows down
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1117702347.22178.5.camel at vangogh>
> Content-Type: text/plain
> > >
> > > Hard to say, check energy and density anyway.
> > Energy and density are normal.
> > > Which gromacs version? Is the machine out of memory?
> > v3.2, memory is fine.
> > > Are there other jobs running (run top).
> > nope.
> > > > >
> > > > > > /Jason
> > > > > --
> > > > > David.
> > > > >
> > As I mentioned before, the only abnormality I can see are the constraint
> > warnings in the log file. Could it be that mdrun is spending more and more
> > time in constraint iteration loops?
> No, it is not iterative.
> Try breaking the jobs in pieces of a few ns. Did you use shuffling or
Well that will take some time. Why do you think that might have an effect?
This run is not parallel, so that answers your shuffling/sorting question.
I just realized that I previously misread the time estimate because I
didn't look at the year - 2006. That makes the change seem much more
reasonable, from 370 to 480 days. This squares with the rate that I
estimated from md.log of 192 ps/day.
> > /Jason
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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