On 10/31/2010 08:20 PM, Valeria Losasso wrote: > Dear all, > for my cluster analysis I am using the g_cluster tool with the gromos method. > The problem is that I have to compare the results for system of different > lengths, and of course the result of the cluster analysis changes according > to the cutoff chosen. So what will be a great choice in this case? > I was thinking about different possibilities, namely: i) choosing - as it is > quite frequent in the literature - an arbitrary cutoff (like the default > 0.1), but using the same for different systems would be probably not > suitable... > ii) looking for every case at the RMSD distribution and choosing the minimum > value between the two peaks - in this case the cutoff would vary for every > system; iii) choosing for every system the cutoff that allows to have in the > largest cluster the 50% of the structures, and also in this case the cutoff > would be different for the different cases... > > Any hint? > Thanks a lot, > Valeria > > > Option ii) is the right one.
Fabio -- ********************************************* Fabio Affinito, PhD CINECA SuperComputing Applications and Innovation Department - SCAI Via Magnanelli, 6/3 40033 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
