AW: [gmx-users] relaxing proteins gradually - how to set constraints?

[Mark Abraham]

Sebastian Kruggel wrote:
> Hi Bjoern
> 
> thanks a lot, for the hint, I tried to freeze the (default-)group Protein-H
> and also a CL- I had to add before with genion, so my em.mdp looks like
> 
> ...
> freezegrps     = Protein-H CL-
> freezedim      = Y Y Y Y Y Y
> ...
> 
> I just wonder why grompp says
> 
> ...
> Freeze       has 3 element(s): Protein-H CL- rest
> ...
> 
> Because that way there isn't much left to minimize ?!

All the tutorial material I've ever seen suggests the use of position 
*restraints*, like Justin suggested. In GROMACS, "constraints" are 
different from "restraints". If the groups you're trying to avoid moving 
are actually in an OK configuration, then there's not much to choose 
between the two approaches. However pdb2gmx generates posre.itp to make 
your life easy with the restraints approach - see 
http://wiki.gromacs.org/index.php/position_restraints

Mark