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.
Quoting Marcelo Fabricio Masman <[EMAIL PROTECTED]>:
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 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
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