Hi James, PCA on a trajectory is about fluctuations -the correlation between deviations from an average positions-, NMA is about penalized displacement -the increase in potential energy due to concurrent displacement-. In NMA the lowest mode is that for which most atoms can move most unrestrictedly. It seems evident that the side chains will severely penalize the displacement of c-alpha atoms. I wouldn't call that a solvent effect or damping. It's the nature of the protein, and the error you make in your model when restricting to c-alpha atoms only.
With respect to the other question, I think the best I can do is to urge you to read more on principal component analysis, until you understand the meaning of 'principal component', 'eigenvalue', 'score', 'projection' and 'loading' :) Cheers, Tsjerk On Thu, Nov 10, 2011 at 8:51 AM, James Starlight <jmsstarli...@gmail.com> wrote: > Hi Tsjerk, > > Thanks for help. So as I understood if I want to calculate fluctuations only > for Calpha I must first to do NMA of my reference in some mode subspace > consisted of the eigenvectors for Calpha atoms only. Does this correct ? > Previously I've done something like this for random subspace of modes in > MMTK (just to reduce the space for calculation) but how perform such > operation in Gromacs I havent known yet :) > > >> The c-alphas are less hindered in the second model due to the absence >> of the side chains and such. There's just more freedom. >> > > It's known that solevnt for instance could significant damp motions from > normal modes. So in my case It seems that sidechains act as the solvent. How > do you think may sidechains not only damp motions oberved for C-alpha atoms > merely but also change the trajectory of their motion? > > > James > > > -- > 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 > -- 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 -- 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
