[gmx-users] Freezing part of the molecules!!!
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jun 7 19:27:50 CEST 2006
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,
Just as a warning: please note that combining:
constraints + freeze groups + pressure coupling
will give undefined results.
> Quoting Marcelo Fabricio Masman <mmasman at gmail.com>:
>>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
> This mail sent through IMP: http://horde.org/imp/
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users