Dear all, 1. For the cluster analysis, I am using the gromos method with cutoff 0.25 nm. With this cutoff I got 201 structures for the lowest temperature for trajectories that are continuous in time (after using demux.pl) The rmsd ranges from 0.073 to 1.55nm.
If I reduce the cutoff to 0.1 nm I will get 1919 structures, which is very close to the total number of frames, 2001 in the .xtc file. This doesn't make sense as I am getting one structure for each frame. Here 1 frame corresponds to 0.01 ns My question, with the cluster analysis, do you fix the value of cutoff or you change cutoff to get a certain number of structures? Following is the syntax I used: g_cluster_mpi -s PRO0.gro -f redPRO0.xtc -method gromos -sz clustsize0.xvg -o clusters0.xpm -g cluster0.log -clid clusidovertime0.xvg -cl out0.pdb -cutoff 0.25 2. For replica exchange,is it better to do the cluster analysis on trajectories that are continuous in ensemble or trajectories that are continuous in time (after using demux.pl) I tried both ways: For replica 0 (for trajectories that are continuous in ensemble, at lowest temperature 300 K), I got two structures with cutoff 0.25 For replica0 (for trajectories that are continuous in time), I got 201 structures with cutoff 0.25 Thanks in advance for your help. thanks, Shyno -- Shyno Mathew PhD Candidate Department of Chemical Engineering Graduate Assistant Office of Graduate Student Affairs The Fu Foundation School Of Engineering and Applied Science Columbia University -- 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 [email protected].
