[gmx-users] Freezing part of the molecules!!!

MGiò magiofer at gmail.com
Wed Jun 7 16:28:06 CEST 2006

just make an index file (make_ndx) custom-defining the groups which you need
to freeze, in your case the C-alpha of residues 18-42. Remember that, when
you define new groups, you should delete the corresponding atoms from the
group that contains all the rest of the protein atoms, if not you'll get an
error saying that a particular atom belongs simultaneously to different
freezing groups.
Hope it helps,


On 6/7/06, Marcelo Fabricio Masman <mmasman at gmail.com> wrote:
> 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
> _______________________________________________
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060607/377abf9b/attachment.html>

More information about the gromacs.org_gmx-users mailing list