[gmx-users] Freezing part of the molecules!!!

[Soren Enemark]

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> Soren Enemark wrote:
> >  Hi Marcelo,
> >  what you need to do is:
> > 
> >  1. create an index file (.ndx) with the groups that you want to freeze.
> >     Such an index file should look like:
> >     [ Group1 ]
> >     45 46 47 48 49 ...
> >     [ Group2 ]
> >     106 107 ...
> >     [ Group3 ]
> >     ....
> > 
> >     where atoms number 45, 46, 47, 48, and 49 etc belong to your 1st group
> and 
> >     so on. Remember to use the numbering as it is in the gro file.
> >     This you can do with "make_ndx -f your_gro_file.gro"
> > 
> >  2. Add the folling to your mdp file:
> >     freezegrps = Group1 Group2 Group3 Group4 Group5
> >     freezedim  = Y Y Y  Y Y Y  Y Y Y  Y Y Y  Y Y Y
> > 
> >     Note that for each group defined as freezegroup you need to specify
> the
> >     dimensions that you want to freeze (x y z). This is done with either
> >     Y or N. So if you want only to freeze Group1 in the z-direction you
> write:
> >     freezegrps = Group1
> >     freezedim  = N N Y
> > 
> >  All the best,
> >  Soren
> > 
> 
> Just as a warning: please note that combining:
> constraints + freeze groups + pressure coupling
> will give undefined results.
> 
 Aha! Is there any particular reason for that, or is it simply because
 the 2 adjustments (constraints and pressure coupling) are difficult for
 the algorithms when combined with the freezed group?

 -Søren


> 
> 
> > Quoting Marcelo Fabricio Masman <mmasman at gmail.com>:
> > 
> > 
> >>Hi all!!!
> >>
> >>I am trying to run a MD simulation with part of my system frozen. I was
> >>looking into the manual but I couldn't find the answer since the manual
> says
> >>the way for freezing complete groups. I would like to freeze only a part
> of
> >>my protein and permit the completed optimization of the rest. For example,
> >>my protein group has 5 protein chains with 42 residues each of them. I
> would
> >>like to freeze (in all directions) the alfa Carbon atoms for residues
> 18-42
> >>for each chain. Does somebody know if it is possible to do such thing with
> >>GROMACS? Can somebody help me?
> >>
> >>Thanks a lot, in advance
> >>
> >>Marcelo
> >>
> > 
> > 
> > 
> > 
> > 
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> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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