[gmx-users] Protein blowing apart

[Gia Maisuradze]

David,

Thanks for your reply.

Ok well yes there are strong interaction pairs.  The structure is:
(CH3)2-CO-/NH-CHCH3-CO-ALA-CO-NH-CCH3-CO/-NH-CH3
The slashes indicate the custom groups that I added.  When I assemble
this protein from a pdb file, it does not add bonds to the two ending
groups.  Instead I go in to the *.top file and add bonds and angles.
It also probably does not add pairs between these groups and the ALA's
in the main chain.
I have tried adding in pairs myself, which makes the calculation crash
after 1-2 ps, and I've tried removing pairs, which does the same.  Not
really sure what else to do.

Thanks,

Gia Maisuradze

----- Original Message ----- 
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, September 12, 2005 11:32 PM
Subject: Re: [gmx-users] random protein breaking


> 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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> -- 
> 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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