Dear All, I am working on a Coarse Grained model (Martini force field), I have a trajectory file and I am trying to do a clustering procedure using the gromos method, this is the command line I used
g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos -skip 10 and it finished well, I got more than 40 clusters, of course if I vary the cutoff this number changes but I am not sure what is the more optimal value for my system. In fact I dont understand very well what is the meaning of this parameter. I have read this "gromos: use algorithm as described in Daura et al. (Angew. Chem. Int. Ed. *1999*, 38, pp 236-240). Count number of neighbors using cut-off, take structure with largest number of *neighbors* with all its neighbors as cluster and eliminate it from the pool of clusters. Repeat for remaining structures in pool." But still...what neighbors means in this context? If someone can clarify this for me, I'd really appreciate it. (I cant acces to the original publication). Thanks in advance. Adriana -- 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.