Hi Tsjerk Many thanks for your kind response. Got the script, will try to run it. Also thanks for clarifying RMSIP vs Cosine content values.
Regards Vijayan.R On Thu, Jun 28, 2012 at 10:56 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Vijayan, > > There must be a script somewhere in the archives > (http://www.mail-archive.com/gmx-users@gromacs.org/msg02871.html) that > calculates the RMSIP from the XPM file of eigenvector inner products. > >> I have come across many papers where they employ RMSIP to quantify the >> similarity between PC1 and PC2 derived by essential dynamics and in >> turn use the values to prove the convergence of conformational >> sampling. Is this a well settled proposition to drive home the point >> that the simulation has converged or should i compute the cosine >> content to prove the same. Which of this is a superior metric ? > > The RMSIP only indicates whether the subspaces sampled are similar, > nothing about the extent of sampling, and nothing about the > convergence. The "essential subspace" (ugh, ugh, cough!, pardon me) > usually converges much faster than the sampling. And the cosine > content... Well, it will show you whether the simulation did not yet > converge. Check some recent replies I gave on the list about that. > > Cheers, > > Tsjerk > > > >> >> >> Thanking in advance >> >> Regards >> Vijayan.R >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Only plain text messages are allowed! >> * 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 > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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
