[gmx-users] Re: PME slows down

[Jason de Joannis]

> 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
> sorting?
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.
> ________________________________________________________________________
> 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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>