[gmx-users] LINCS warnings for O-P-O-H bond
spoel at xray.bmc.uu.se
Tue Feb 11 20:12:57 CET 2003
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.
> > > 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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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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