[gmx-users] cut in gmx clustsize

[Alex]

Dear all,
In clustering what is usually defined as a criteria is a cut-off so that if
two atoms or molecules are closer to each other less than the cut-off then
those two are being counted to be in a cluster, I see even that in the
source code of gmx clustsize where
...
/* If distance less than cut-off */
if (bSame)
{
/* Merge clusters: check for all atoms whether they are in
* cluster cj and if so, put them in ci
*/
for (k = 0; (k < nindex); k++)
...
However, what is puzzling me is the definition of the -cut as "Largest
distance (nm) to be considered in a cluster" in gmx clustsize man page.
So, would you please elaborate that further?

Also, how the default cut-off of 0.35 nm has been indicated?

And finally, in the case of using -mol option to consider the molecules
rather than atoms in clustering, I wonder if the cut-off is the distance
between center of mass of the molecule?

Regards,
Alex