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 > > > > 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 > >> > > > > > > > > > > > > ------------------------------------------------- > > This mail sent through IMP: http://horde.org/imp/ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > 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 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
