[gmx-users] defining group

[Omer Markovitch]

Thank you both! Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Sat, Sep 13, 2008 at 15:57, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Omer Markovitch wrote:
>
>> Hello,
>> I would like to ask for your help in defining groups:
>> Say I have a protein. I would like to have two groups (1) the Calpha
>> backbone (2) everything else.
>> Later on, I will want to freeze the Calpha group.
>> How can I define these groups? Where?
>> I have looked in the manual, but I do not understand how to do it and in
>> which files.
>>
>
> Groups are defined in index files (.ndx), which are created with make_ndx.
> Calpha is a default group read in from a protein structure.  To create a
> group that is everything but Calpha (group 3 in the make_ndx list), you
> would use
>
> !3
>
> at the make_ndx prompt.
>
> -Justin
>
>  Thank you, Omer Markovitch.
>>
>> Koby Levy research group,
>> Weizmann Institute of Science.
>> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> 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
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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/20080913/35cbaf2f/attachment.html>