Can you use this freezegroups function during a minimizaiton? (say if
you wanted to minimize solvent around your protein, while keeping the
protein fixed?)
David van der Spoel wrote:
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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