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

[Anton Feenstra]

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
> 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 |
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