Hi Tsjerk Many thanks for your response. Do you think NMA is worth considering in such cases like this?????
Regards Vijayan.R On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > 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 >
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