[gmx-users] ED analysis: help on cosine content and overlap of the fluctuations

[Caterina Arcangeli]

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 <caterina.arcangeli at casaccia.enea.it>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> 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    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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