I want to analyze water cluster formation in my (polymer/water) system. I used following command:
gmx clustsize -f npt2.xtc -s npt2.tpr -o csize.xpm -nc clust.xvg -ac average.xvg -b 90000 -e 100000 -cut 0.37 -n watercluster.ndx
Total number of water molecule is 1920. But, average number of clusters is 50 and average cluster size is 60.( fluctuations is not high). When I multiply average number of clusters to average cluster size I should have a number near total water molecule. But, it is 50*60 =3000 which is very far from total water molecule(1920!). What’s more, when I check Cluster size distribution using
-hc histo.xvg It doesn’t give me a meaningful result. For all of my systems with different water content cluster size distributions are the same nearly, like I attached here, which is not what I expect and it’s peak is far from average cluster size for each sytem . how can I interpret it? what is the problem?
Thanks alot for your help.