Dear GROMACS users,
I am attempting to compute the number of water clusters within a zeolite structure (Zeolite + Water system). I used the following command for this purpose:
gmx clustsize -f nvt_10000ps_10000.trr -s nvt_10000ps_10000.tpr -nc cluster_Wat_50_Replacement.xvg -cut 0.35 -b 7000 -e 9500 -n OW-OW.ndx
The output provides several metrics, including the number of clusters and the average cluster size. My understanding is that a cluster is formed when at least two water molecules are within the predefined cutoff distance. However, my system contains 400 water molecules, yet the reported number of clusters is 289. This seems counterintuitive; even if all water molecules formed pairs (i.e., clusters of two), I would expect a maximum of 200 clusters.
Could you please help me understand this discrepancy? Is there a nuance in the definition of a water cluster within gmx clustsize that I am overlooking, or could there be an issue with my understanding or methodology?
Thank you for your time and assistance.