[gmx-users] LINCS warnings for O-P-O-H bond
Luciane Vieira de Mello
mello at cenargen.embrapa.br
Tue Feb 11 20:06:30 CET 2003
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.
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?
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| 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/ |
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