Thanks Tsjerk On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Vijayan.R, > > Not really. NMA also assumes linear relationships. > > Cheers, > > Tsjerk > > On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan <biovija...@gmail.com> > wrote: > > 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 > > > > > > > > -- > > 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 >
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