[gmx-users] defining group

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 13 14:57:17 CEST 2008

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


at the make_ndx prompt.


> Thank you, Omer Markovitch.
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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