Hi vivek, I have few questions related to your query:
During covariance matrix calculation, g_covar by default takes average structure of the trajectory as a reference structure then why you are giving it average structure of your trajectory (0-100ns) manually. Moreover without looking at your commands which you have used, it would be difficult for anyone that why are you getting these surprising results. On Thu, Feb 7, 2013 at 1:26 PM, vivek modi <modi.vivek2...@gmail.com> wrote: > Hello, > > I have troubled you with a similar question before also, but I guess I need > some more clarification. My question is about the reference structure in > PCA analysis. > I have 100ns long protein simulation which I want to analyze using PCA. The > RMSD shows fluctuations upto initial 25-30ns and then becomes very stable. > I have performed PCA on the last 30ns window of the simulation where I > assume the simulation has converged (I also did on other time windows as > well). > > The question is this: > I did the analysis on the last 30ns window in two ways by taking two > different reference structures. > > a. I take the average structure of the trajectory (0-100ns) as > the reference and then do the fitting and calculate covariance matrix for > last 30ns. This is done because I suspect that the average structure over > full trajectory will reflect all the changes occurring in the protein. It > also gives me low cosines (<0.1). The PCs show movement occurring in > certain regions of the protein. > > b. I take the average structure from the same window (last 30ns) then do > the fitting and calculate covariance matrix for the same. This is done with > an assumption that the reference structure must reflect the > equilibriated/stable part of the trajectory unlike the previous case. > Surprisingly it gives me high cosines (>0.5). Unlike the previous case, > this method shows very small movement in the protein (very low RMSF). > > Both of these methods give me different RMSF for the PCs although they are > done on the same part of the trajectory but the reference structure is > influencing the output. > > Which protocol among the two is appropriate ? And how can we explain high > cosines in second case where the reference structure is the average of the > same time window (there must not be large deviation) while I get low cosine > for the first case where deviations are calculated from the full trajectory > average (large deviation) ? > > Any help is appreciated. > > Thanks, > > -Vivek Modi > Graduate Student > IITK. > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- *----------------------- Thanks and Regards, Bipin Singh* -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
