[gmx-users] random protein breaking

[Gia Maisuradze]

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.

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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