Thanks a lot Tsjerk. I really appreciate the help.
Regards, -Vivek. > Message: 6 > Date: Tue, 1 Nov 2011 17:35:54 +0100 > From: Tsjerk Wassenaar <[email protected]> > Subject: Re: [gmx-users] PCA on secondary structure of protein. > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <cabze1sisyaawp1wx43bygbqcfr5wa47mto13vzhgd+sd7mr...@mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Sure! > > You'll just be looking at correlations between secondary structure > elements, disregarding the role that the loops may play. But it's a > sound approach. > > :) > > Tsjerk > > On Tue, Nov 1, 2011 at 3:44 PM, vivek modi <[email protected]> > wrote: > > Hi, > > > > I plan to perform PCA on a globular protein which I am studying. The > > simulation for the same is done for 100ns. > > I have small doubt. Is it appropriate to perform PCA to study the > movement > > in protein on only secondary structure elements (helices in this case). > > My protein contains long loops which do not play any role. Is it > appropriate > > to group only the helices together ignoring the loops and perform PCA ? > > > > Any help is appreciated. > > > > > > Regards, > > > > -Vivek Modi > > Graduate Student > > IITK. > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > > > ------------------------------ > >
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