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Hi,<br><br>The cosine content is not the most important property you should look at.<br>Like any type of analysis, you should check the convergence.<br>The simplest way of doing this is cutting your trajectory in, for instance,<br>four parts and determining the correlation.<br>g_anaeig will always print the covariance matrix overlap when two eigenvector<br>files are provided.<br><br>Note that PCA by itself does not do any interpretation.<br>One can always perform PCA on any length of trajectory.<br>In most cases the first PC's will be the slowest converging<br>properties of a system. But is it up to the scientist to properly<br>interpret the results. In many cases there might not be a lot<br>of useful information. On the other hand, if you are looking<br>for a specific effect there might be.<br><br>Berk<br><br>> Date: Sun, 11 Jan 2009 18:51:03 +0000<br>> From: t.piggot@bristol.ac.uk<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] eigenvalues<br>> <br>> So just to make sure i got this correct, when looking at the cosine content <br>> of the principal components i should look at the whole trajectory? Do i <br>> need to include the initial relaxation in the first few ns of the <br>> production simulation?<br>> <br>> If there is a high cosine content for the whole trajectory is there <br>> anything else to be done (if i want to look at the low frequency motions of <br>> the trajectory) except for simulate for longer (i have a very large system <br>> so not the favoured option!)?<br>> <br>> As you say it seems that lots of people use PCA on short trajectories, even <br>> of large systems, which to me is confusing<br>> <br>> Thanks for any insights you can give<br>> <br>> Tom<br>> <br>> --On Saturday, January 10, 2009 11:49:18 +0100 Tsjerk Wassenaar <br>> <tsjerkw@gmail.com> wrote:<br>> <br>> > Hi Sanjay,<br>> ><br>> > Imagine yourself zig-zagging along a line from one place to another.<br>> > If you look at you're motion (and the variance), you'll find that if<br>> > you only look at blocks most of it is explained by the zig-zag and<br>> > nicely periodic (no cosine content as in Berk Hess' paper). Good, you<br>> > think. But if you look at the whole travel, the most important<br>> > contribution is the going from one place to another, and if you look<br>> > at you're displacement over time with respect to the mean, that will<br>> > give you half a cosine. The fact that results in a block do not fit a<br>> > cosine does not take away the fact that you're still in the process of<br>> > relaxation. I know it's not what you want to hear, but I've seen it<br>> > happen to a complex of >600 residues, where relaxation took more than<br>> > 30 ns. I also know that people often do PCA on short time<br>> > trajectories, but it's not the proper thing to do.<br>> ><br>> > Cheers,<br>> ><br>> > Tsjerk<br>> ><br>> > On Sat, Jan 10, 2009 at 7:34 AM, <sanjay23@iitb.ac.in> wrote:<br>> >> Hi Tsjerk,<br>> >> thanks<br>> >> actually my protein is quite larg (509 aa).i had divided my trajectory in<br>> >> different part and according to your suggestion i calculated<br>> >> cosine-content for all, and find that trajectory from 5to15 ns and<br>> >> 18to25ns having cosine value very less about 0.03 in both cases(with and<br>> >> without ligands), while other combination showing higher values (>0.6).so<br>> >> i think my system is Ist converges around 5ns and maintaining it up to 15<br>> >> ns after that it may be few conformational fluctuation occurring and<br>> >> finally it get stabilized from 18to15ns.may that part 15to18ns trajectory<br>> >> is transition period between to conformational fluctuation. i have also<br>> >> calculated temp. and pressure during whole simulation and i find that it<br>> >> is exact Gaussian between 5to25ns.so my confusion is whether i take my<br>> >> trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25,<br>> >> but 5to25 showing value of cosine >0.6.<br>> >><br>> >> _______________________________________________<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> >> Please search the archive at http://www.gromacs.org/search before<br>> >> posting! Please don't post (un)subscribe requests to the list. Use the<br>> >> www interface or send it to gmx-users-request@gromacs.org.<br>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> >><br>> ><br>> ><br>> ><br>> > --<br>> > Tsjerk A. Wassenaar, Ph.D.<br>> > Junior UD (post-doc)<br>> > Biomolecular NMR, Bijvoet Center<br>> > Utrecht University<br>> > Padualaan 8<br>> > 3584 CH Utrecht<br>> > The Netherlands<br>> > P: +31-30-2539931<br>> > F: +31-30-2537623<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> <br>> ----------------------<br>> TJ Piggot<br>> t.piggot@bristol.ac.uk<br>> University of Bristol, UK.<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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