[gmx-users] about minimization

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Fri Mar 22 15:58:41 CET 2002

> Is it possibly a problem with constraints? The default Gromacs parameters
> will turn bonds into constraints and constrain those using Lincs, also
> during EM. But for CG/NM type of calculation, the default 4th order for
> Lincs is not sufficient. In that case, try 8 or 12...

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?

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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