I thank Ran and Berk for useful and critical discussion. Caterina
> I agree with Ran. > > But on your quesion of inconsistency. > It seems like your essential subspace (the space spanned by > the first 10 eigenvectors) has converged. > But this does not say much about the convergence of the > first few eigenvectors in this subspace. >> From the cosine content one can clearly say that M1 is not > converged. Since M2 is a subset of M1 it is also not converged. > So for proper sampling of global conformations you would need > to simulate several orders of magnitude longer, > as one would expect for a 253 residue protein. > If you need this for what you are interested in is another question. > > Berk. > > >> From: Ran Friedman <[EMAIL PROTECTED]> >> Reply-To: Discussion list for GROMACS users <[email protected]> >> To: Discussion list for GROMACS users <[email protected]> >> Subject: Re: [gmx-users] ED analysis: help on cosine content and >> overlap ofthe fluctuations >> Date: Fri, 13 Apr 2007 13:44:19 +0200 >> >> Dear Caterina, GMX users, >> >> It's very difficult to decide whether a simulation converged, at least >> for macromolecules. There are a lot of studies in the literature about >> it, but there's no concrete answer. I'd try to ask when the results can >> be useful, and not when the simulation (or PC) converged - and that >> depends on your system and what you are trying to model. One hint is >> that a PC with a high cosine content is probably not going to be very >> useful if you try to simulate any kind of structural transitions. >> >> Ran. >> >> Caterina Arcangeli wrote: >> > 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 >> > >> > >> >> >> -- >> ------------------------------------------------------ >> Ran Friedman >> Postdoctoral Fellow >> Computational Structural Biology Group (A. Caflisch) >> Department of Biochemistry >> University of Zurich >> Winterthurerstrasse 190 >> CH-8057 Zurich, Switzerland >> Tel. +41-44-6355593 >> Email: [EMAIL PROTECTED] >> Skype: ran.friedman >> ------------------------------------------------------ >> >> _______________________________________________ >> 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 > > _________________________________________________________________ > Play online games with your friends with Messenger > http://www.join.msn.com/messenger/overview > > _______________________________________________ > 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
