[gmx-users] LINCS Warnings in the middle of an MD run

[K.A.Feenstra]

David van der Spoel wrote:
> 
> On Fri, 14 Dec 2001, K.A.Feenstra wrote:
> 
> >[.. after reading David's comment, I felt I could add something more...]
> >
> >This is a 'normal' error, in the sense that a rotatable group like
> >your protonated NH3 group in the lysine sidechain, can build up a large
> >rotational velocity. Since this motion couples only weakly with the
> >rest of the system, once you have the high rot. velocity, it stays there
> >for some time. If the velocity builds up too high, lincs will get problems
> >re-setting the bond lengths that get elongeted due to centripetal forces.
> >There is a finite chance to get this buil-up, which obviously increases
> >with simulation length...
> I'm not entirely convinced. The NH3 should probably be hydrogen bonded to
> something, and in that have quite strong forces on them. Furthermore there
> is also a weak dihedral force (which is periodic of course). The only way
> in which such rotation could be maintained is when it rotates by 120
> degrees (around the CE-NZ torsion) in one step. In that case
> electrostatics does not change. However, that seems quite unlikely to
> me... As a remedy maybe one could increase the torsional barrier, or
> obviously use shorter timesteps...

OK, let's conclude by saying that this is a much debated issue on which
opinions vary...

-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
| / \ / \'| | | Tel +31 50 363 4327                    Nijenborgh 4 |
|(   |   )| | | Fax +31 50 363 4800               9747 AG Groningen |
| \_/ \_/ | | | http://md.chem.rug.nl/~anton        The Netherlands |
|             | "Fly to the Court of England and Unfold" (Macbeth, A|
|_____________|_____________________________________________________|