[gmx-users] Freezing part of the molecules!!!
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jun 7 23:59:54 CEST 2006
Soren Enemark wrote:
> 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
>>> 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
>>> 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
>>> freezegrps = Group1
>>> freezedim = N N Y
>>> All the best,
>>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?
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 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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