[gmx-users] LINCS warnings for O-P-O-H bond
feenstra at chem.vu.nl
Tue Feb 11 13:19:18 CET 2003
Luciane Vieira de Mello wrote:
> Dear all,
> 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
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 |
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