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
