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

Soren Enemark soren.enemark at polimi.it
Wed Jun 7 18:32:42 CEST 2006

 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,

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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