[gmx-users] random protein breaking

[David van der Spoel]

On Mon, 2005-09-12 at 15:01 -0700, Gia Maisuradze wrote:
> Hi,
> I'm running a self made protein, three ALA's and two custom ending groups. 
> At random times the full dynamics runs fail.  Sometimes as short as 90 ps 
> sometimes as long as 16 ns.  This is the error:
> t=sometime Water molecule starting at atom X can not be settled.  Check for 
> bad contacts and/or reduce the time step.
> Large CVM(group rest): Xxxxxxxxx - some ridicuously large number.
More info please.

Any strong intramolecular interaction in the custom groups?

(e.g. COOH)
> 
> I also noticed that the protein usually breaks at the custom end groups, 
> I've tried changing the bond parameters, but still this error persists. 
> Also I have used a time step as short as 0.0005 and still get this error.
> 
> Does anyone have idea why it happens?
> 
> Thanks,
> 
> Gia Maisuradze
> 
> 
> ----- Original Message ----- 
> From: "Gia Maisuradze" <gia at chem.unr.edu>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Monday, September 12, 2005 12:53 PM
> Subject: Re: [gmx-users] Slow opterons : low Mega Flops
> 
> 
> > Hi,
> > I'm getting really slow performance on my opteron system, performance that 
> > is roughly half that of my old athlon mp system.  I've tried recompiling 
> > the program with various options, mpi, no mpi, threading, no threading, 
> > cpu optimized, not optimized, etc.  Does anyone work with opterons under 
> > suse 9.3 and have an idea about what the best options for compiling lam, 
> > fftw, and gromacs should be?
> >
> > Thanks,
> >
> > Gia Maisuradze
> > _______________________________________________
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> 
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-- 
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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