[gmx-users] Protein blowing apart

[Gia Maisuradze]

Do you mean I should make the whole protein as one block in the rtp, or add 
pairs to the end units I've made in the rtp file?

Thanks,

Gia Maisuradze

----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, September 14, 2005 1:22 PM
Subject: Re: [gmx-users] Protein blowing apart


> 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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> -- 
> 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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