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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