Soren Enemark wrote:
Quoting David van der Spoel <[EMAIL PROTECTED]>:
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
It's an ill-defined situation, you will get NaN pressure. You can either
turn off the constraints on the atoms that are frozen (but then what are
you doing?), or turn of pressure coupling.
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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