Hi Anna, On Thu, Jul 21, 2011 at 5:11 PM, Anna Marabotti <anna.marabo...@isa.cnr.it> wrote: > Thanks Mark for suggestion, I'll try to do a simpler clustering method. In > the meantime, I only would like to add a further info: I pre-processed my > trajectory following someone's (Justin, IIRC) suggestion in a previous > message, using trjconv -pbc mol -ur compact. So, in my trajectory the > molecules should be whole (at least, I see my protein as a whole). This > pre-processing was necessary because with trjconv -pbc whole I was not able > to have my homodimeric protein in the unit cell: the protein was split in > two monomers in two adjacent unit cells. Could be the presence of the two > identical monomers to "confuse" Gromacs that sees an RMSD minimum of 0? > Anna
No, the output says the RMSD ranges from 0.07 to 0.28. The problem arises because you only get one cluster using a cutoff of 0.25 nm. If you're certain there are some clusters to be identified, despite the low RMSD values that sort of indicate there is not much variation, then you can lower the cutoff. The error also does not pertain to the RMSD matrix, but probably to the matrix of transitions, because there aren't any. Please do note that this has absolutely nothing to do with using a rhombic dodecahedron :p Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
