[gmx-users] Re: Lincs

[Anton Feenstra]

"David L. Bostick" wrote:
> 
> Hi Anton,
> 
> I was curious...  You said before..
> 
> > longer time steps. Generally speaking, the Lincs constraints algorithm
> > will be more stable, and definitely is faster, but it is unable to
> > handle the highly connected network of constraints in CCl4.
> 
> What sort of things can the Lincs algorithm handle.  Can it handle things
> like proteins?  I have been using it for proteins.  Is this a bad idea?

Proteins are no problem, it was in fact designed more or less with
proteins in mind. Problems arise with so-called highly connected
constraints. The simplest example of this is a united-atom model
of butane, i.e. four particles in a row with bonds and angles and
only a single dihedral. If you want to constrain both bond lengths
and angles in butane, you have a sort of double triangle construction, 
like:
	C-C.
	 `.\`.
	   `C-C
The problem can be illustrated by considering the correction applied 
to both angle constriants (here the 'dotted lines'): correcting these
will also affect the length of the middle C-C bond. As this will also
get its own, proper, correction, the result is an over-correction.
In shake actually similar things play, but there it is solved
iteratively,
which also takes care of this over-correction. Lincs is non-iterative
by design, and hence will fail in these situations. These normally only
occur when both bond lengths and angles are constrianed, which is not
sensible for proteins.

(Hmm. I'm in the lecturing mood today, it appears...)

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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