[gmx-users] Freezing part of the molecules!!!
soren.enemark at polimi.it
Wed Jun 7 23:27:31 CEST 2006
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,
> > 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?
> > Quoting Marcelo Fabricio Masman <mmasman at gmail.com>:
> >>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
> >>the way for freezing complete groups. I would like to freeze only a part
> >>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
> >>like to freeze (in all directions) the alfa Carbon atoms for residues
> >>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
> > 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 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
> 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
This mail sent through IMP: http://horde.org/imp/
More information about the gromacs.org_gmx-users