Hi Vivek, The high cosine content of the first pc indicates that the system is still equilibrating. You're sort of still on the road from A (the starting position) to B (the equilibrated state).
Hope it helps, Tsjerk On Oct 20, 2011 5:07 PM, "vivek modi" <modi.vivek2...@gmail.com> wrote: Hi Tsjerk, Thanks a lot for your reply. But now I will ask a very naive question. My study involves understanding the dynamics of a group of closely related proteins. All of them are simulated for a period of 100ns each. I have also analyzed the RMSD using g_rms for all of them and it becomes very stable after 20-30ns for all the proteins. But when I do PCA I see high cosines (~0.8) for the first PC. For all the other PCs the cosine content is very low. The question is that is it appropriate to ignore the first PC and make inference about the motion of the protein by using other PCs ? Thanks a lot. Regards, -Vivek Modi Date: Wed, 19 Oct 2011 13:58:00 +0200 > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] Reference structure for g_covar > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CABzE1SjU=n78nwo+o0utm7ovdwz4hbgjeylj8x0nbwewwlz...@mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Hi Vivek, > > I explained related matters in some detail on this list > earlier, and > would urge... > -- 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
