Hi all, I want to calculate the number of clusters of my glycine molecules during the course of my simulation. I have read that gmx clustsize is the correct command to use. I read on one of the previous threads that I will have create a separate tpr file for the molecule of interest. And I had to generate another trajectory file in order for them to match. I run the command below:
gmx clustsize -f glycine.xtc -s glycine.tpr -nc nclust.xvg -b 0 -e 60000 -cut 0.35 -mol I get an error message saying that gromacs only finds 1 cluster but this cannot be right as I can see more than one cluster forming during the simulation Fatal error: Lo: 0.000000, Mid: 1.000000, Hi: 1.000000 Can somebody please advise me on how to overcome this issue? Many thanks, Akash -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
