[gmx-users] LINCS warnings for O-P-O-H bond

[David]

On Tue, 2003-02-11 at 20:06, Luciane Vieira de Mello wrote:
> Dear Anton,
> 
> Thanks for your quick reply. I have tried your suggestion: "change the
> mass of the hydrogen from 1 to e.g. 4 to reduce
> its 'jittery' behaviour"
> But unfortunately it hasn't worked very well. I tried a short relax_md and
> still got the LINCS warning including the same atoms.
You want to remove the 1-4 interaction between H and O in the phosphate
group. Check under the pairs section.

> 
> Step 4062, time 8.124 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 8.816363 (between atoms 603 and 604) rms 0.123279
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     600    601   90.7    0.1480   0.2709      0.1480
>     600    603   49.1    0.1610   0.1580      0.1610
>     603    604   90.2    0.1000   0.9816      0.1000
> 
> And even worse, I got a segmentation fault this time.
> 
> I am thinking of restrain the dihedral angle envolving these atoms. Do you
> think it would be a good strategy?
> 
> thanks in advance.
> 
> Luciane
> 
> > > I've added a singly negatively charged phosphoserine to my GROMACS
> > > dictionary.   All seemed well and the MD runs.  What worried me now are a
> > > series of warnings e.g.
> > [...]
> > > This bond is my O-P-O-H bond in the phosphoserine.  I uncommented the
> > > following line in the ffgmxbon.itp file
> > >
> > >     P   OA    1     0.000       1.046      3
> > >
> > > Is this right?  Or do we not need to worry about a dihedral for
> > > A-B-C-hydrogen?
> >
> > In general, you *would* worry about this. In this case, it is not
> > unsurprising: there is a very light, and charged atom (H) in a heavily
> > charged environment (the O-P-O etc.). Because of this, it will feel
> > very large forces at times, and have quite a bit of chance of starting
> > to spin. Then LINCS feels it is time to warn the user.
> >
> > I wouldn't recommend removing the dihedral. Rather, if you need a fix,
> > you could change the mass of the hydrogen from 1 to e.g. 4 to reduce
> > its 'jittery' behaviour. If you're interested in longer scale (~ns)
> > properties and/or averages, that should still be a-o-k.
> >
> > > Another strange aspect is that it is taking more than a overnight to run
> > > 20ps, what usually takes a couple of hours.
> >
> > Writing text can be very slow. It could be the LINCS warning that slow
> > you down there, perhaps in combination with writing to nfs?
> >
> >
> > --
> > Groetjes,
> >
> > Anton
> >   _____________ _______________________________________________________
> > |             |                                                       |
> > |  _   _  ___,| K. Anton Feenstra                                     |
> > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> > |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> > | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> > |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> > |             | "If You See Me Getting High, Knock Me Down"           |
> > |             | (Red Hot Chili Peppers)                               |
> > |_____________|_______________________________________________________|
> >
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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