[gmx-users] Si-O-Si angle calculation with g_angle

[David van der Spoel]

Tandia, Adama wrote:
> Dear ALL:
> 
> I have used GMX to study SiO2 in a glassy phase. Is it possible to use
> mk_angndx followed by g_angle to have the distribution of the Si-O-Si
> angles in the system?
> I have tried the following and end up with an empty ange.ndx file:
> 
> 	mk_angndx -s silica.tpr -n angle.ndx -type angle
> 
I would suggest writing a script to make the index. You only have to 
supply the atom triplets. The mk_angndx only works with when the exact 
angles are in the tpr file.
> Regards,
> 
> Adama
> 
> ---------------------------------------------------------
> Adama Tandia
> Modeling & Simulation
> Corning INC
>  
> Tel: 607 248 1036
> Fax: 607 974 3405
>  
> www.corning.com
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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