[gmx-users] defining group

David van der Spoel spoel at xray.bmc.uu.se
Sat Sep 13 14:56:43 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?
Using make_ndx
backbone is predefined, e.g. group 4 and protein is usually 1
then you select
1 & !4

> I have looked in the manual, but I do not understand how to do it and in 
> which files.
> 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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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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