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...
Vitaly
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