Hi Vijayan R., > What i infer from this is that the cumulative variance experienced by the > top 10 PC is hardly ~ 30 %.
Not experienced...; It's the variance captured by the first ten PC's. > a) does this imply inadequate sampling by MD or a limited conformational > change happening in the system???? No, not at all. It shows that the motions in your system can not be adequately captured by linear combinations of atom fluctuations. The system may be too flexible and/or there may be a lot of rotational motion. > b) is it wise to consider the Nucleic acid during essential dynamics or > should it be discared and only the Protein BB or CA be considered. Analysis with and without nucleic acids are just two different things. Cheers, Tsjerk -- 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
