Short answer? RMSD is a lousy measure of convergence :) ----- 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
