Dear David sir, Is it feasible to evaluate Gibbs free energy landscape of only the concerned loops from cartesian coordinates? I mean to say is it feasible to extract covariance matrix of my concerned loops from the entire trajectory and then evaluating Gibbs free energy landscape? OR, should I extract trajectories of each and every loops separately and calculating extract covariance matrix of each loop and then should I see the Gibbs free energy landscape?
On Thu, Sep 24, 2015 at 7:42 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 24/09/15 13:54, Nabajyoti Goswami wrote: > >> Sir, >> I am a very big fan of yours and I deeply apologize for mailing this way. >> Actually I need some outcome within a very short period of time. So, I >> could not wait for the mailing lists answers. >> >> Coming to the point.. Can you please explain the tricks of dihedral PCA? >> You answered as my sampling was far from being complete because of the >> huge differences between my chosen temperatures 300K and 310K, then how >> can I make some comments at least, if my results are inconclusive. So >> far as stability point of view, how do I set my MDs? >> > As I said you may be sampling different part of phase space, but it could > also be that it is something very similar in cartesian space. > The simple recommendation is do not use dihedral PCA at all but something > in cartesian space. > >> >> I have attached another figure (3D version of the previously generated >> figure). But I am a bit in confusion to analyze them. >> >> Please help a little sir. >> >> Regards, >> >> Yours truly >> >> >> Nabajyoti Goswami >> >> Bioinformatics Infrastructure Facility >> Department of Animal Biotechnology >> College of Veterinary Science >> Assam Agricultural University >> Khanapara, Guwahati 781022 >> Assam, India >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Nabajyoti Goswami Research Associate Bioinformatics Infrastructure Facility Department of Animal Biotechnology College of Veterinary Science Khanapara,Guwahati 781022 Assam, India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.