[gmx-users] about minimization

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Fri Mar 22 17:46:37 CET 2002

On Fri, 22 Mar 2002, Anton Feenstra 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
> > >applied 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
> intrinsically 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.

Uhm, I thought according to the GMX Manual LINCS was default (p. 28) for
everything including water (p. 29,"The method is more stable and faster
than SHAKE, but it can only be used with bond constraints and isolated
angle constraints, such as the proton angle in OH.", or water molecule
doesn't suffice it?). At p. 86 is said that "SETTLE can be selected in the
topology file."

As far as I know I've never seen a MD programme able to do EM with CG
having freeze groups and constrains.

Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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