[gmx-users] g_clustsize

[David van der Spoel]

Vitaly Chaban wrote:
> RF> In this case, you topology is read from the .tpr file and all of the 
> molecules there are taken into account for clustering.
> 
> 
> I think you are right but the following text from the g_clustsize help 
> message has confused me:
> 
> 
> "
> 
> When the -mol option is given clusters will be made out of molecules rather
> 
> than atoms, which allows clustering of large molecules. In this case an 
> index
> 
> file would still contain atom numbers or your calculcation will die with a
> 
> SEGV.
> 
> "
> 
> 
> So what is the sense to make index.ndx if ALL molecules are used for the 
> calculation always...

Actually the text is incorrect (even the English is weird). If you use 
the -mol flag the program will tell you that the index file is ignored. 
If I recall correctly this wasn't always the case, and you could select 
a subset of the molecules for this analysis. No clue why that disappeared.

> 
> 
> 
> Vitaly
> 
> 
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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