Alan Dodd wrote: > Short answer? RMSD is a lousy measure of convergence :) >
Yes I know :) Indeed, I further applied cluster analysis and ED. My question regards the supposed inconsistency between the results from cosine content and overlap analyses.... Thanks > ----- Original Message ---- > From: Caterina Arcangeli <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <[EMAIL PROTECTED]> > Sent: Friday, April 13, 2007 10:58:54 AM > Subject: [gmx-users] ED analysis: help on cosine content and overlap of the > fluctuations > > > Dear all, > > I performed essential dynamics (ED) analysis on my protein (253 amino > acids). The simulation (10ns) achieves stability in the RMSD after > 6.0ns, but a convergence analysis based on cluster analysis (as > described by Daura, 1999) indicates that the conformational sampling > reaches a stable value only for the last 1.0ns. > > So, I've performed ED on both 6-10 ns (M1) and 9-10ns (M2) time interval > using g_covar. > > To check if the principal modes are well defined, I've calulated the > ovelap of the sampling between the first and second half of the > trajectories (I've splitted M1 and M2 into two halves) and the cosine > content of the first eigenvectors: > - the normalized overlaps are 0.499 (M1) and 0.434 (M2); > - the subspace overlaps (rmsip) for the first 10 eigenvectors are 0.748 > (M1) and 0.686 (M2); > - the cosine content of the first eigenvectors is 0.828 (pc1) for M1 and > 0.125 (pc1) for M2. > > So, apparently, the two method are inconsistent: > a higher rmsip value is observed for M1 (according to Amadei, a rmsip > value > 0.7 shows a reasonable convergence) wheras the lower cosine > content is obtained for M2 (according to Hess, a value < 0.5 indicates > jumping between clusters and not a merely random diffusion). > > My questions are: which time window better describe the dynamics of my > protein? From where come out this inconsistency? What I'm wrong? > Thank to all. > > Caterina > > > > > > P.S. I aware that 10 ns are in general insufficient to describe the > thermodynamics of a protein but I want just to have an idea of some > structural properties of my protein. > > > > > > > > > _______________________________________________ > gmx-users mailing list [EMAIL PROTECTED] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list [EMAIL PROTECTED] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Caterina Arcangeli ENEA, Computing and Modelling Unit (CAMO) Casaccia Research Center - Post Bag 026 Via Anguillarese 301 - 00060 Roma phone +39 06.3048.6898 fax +39 06.3048.6860 http://www.enea.it _______________________________________________ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
