[gmx-users] about minimization

[Anton Feenstra]

David van der Spoel wrote:
> 
> On Fri, 22 Mar 2002, Alan Wilter Sousa da Silva wrote:
> 
> >Gromacs manual p. 33 says (sic) "[...] Conjugate gradient can not be used
> >with constraints or freeze groups."  So what LINCS is?  Moreover, is LINCS
> >aplied to all system? I mean, including water molecules?  If so, when
> >SETTLE is used?

Settle is used for water. Lincs (optionally) for all other bonds.
Lincs is an alternative to Shake, it is non-iterative and therefore
intrisically more stable. It is also faster.


> I think this is correct. It will not converge with constraints.

I don't know exactly, I'm not that familiar with CG.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "I Smell Smoke From a Gun Named Extinction" (Pixies)      |
|________|___________________________________________________________|