[gmx-users] Protein blowing apart

[David]

On Wed, 2005-09-14 at 13:13 -0700, Gia Maisuradze wrote:
> 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.
Make a new building block in rtp file. Then e.g. pairs are generated.
> 
> 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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> >> >
> >>
> >> _______________________________________________
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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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> 
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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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