Because it fits a little bit better to a cosine with full period than the first one fits a cosine with half period and the third one fits a cosine with 1.5 period.
Tsjerk On Mon, Feb 25, 2013 at 1:23 PM, Ahmet yıldırım <ahmedo...@gmail.com> wrote: > Hi, > > I think my question was misunderstood. > My question is: > Why is second cosine content greater than the other values? > > Regards > > 2013/2/25 Thomas Evangelidis <teva...@gmail.com> > >> On 25 February 2013 12:14, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> >> > Hi Thomas, >> > >> > As I've explained previously, the cosine content does not allow such >> > inferences. Besides, taking the relaxation from the start into account >> > in PCA is pretty nonsensical, unless you aim to characterize that >> > relaxation in the first place. Looking at the cosine content to infer >> > >> >> Yes, that's what I meant, to identity those ns where the protein does >> unidirectional motion before it starts exploring the energy landscape, and >> exclude them from the final analysis (whatever this is). At least this is >> what I've seen doing in publications and this is what I have understood >> from our previous conversations. I think your objection is about the way I >> use the term "equilibration" to refer to what you call "relaxation" (I >> presume it is not the same as energy minimization). Perhaps it would be >> helpful to have your definition of the terms "equilibration" and >> "relaxation. >> >> >> > equilibration from that is blatantly fooling yourself. >> > If you feel you must use cosine content to support any claim on >> > equilibration, then it is a much better approach to start from the end >> > of the simulation and check that the stretch of the trajectory you >> > take does not yield high cosine contents, in which case you have some >> > reason to argue that that part of the simulation is sampled in a local >> > equilibrium. >> > >> > Cheers, >> > >> > Tsjerk >> > >> > >> > On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis <teva...@gmail.com> >> > wrote: >> > > You don't do it the right way. You must start the analysis from the >> > > beginning not from the end of your trajectory. I.e. >> > > >> > > 0-20ns >> > > 0-30ns >> > > 0-40ns >> > > ... >> > > 0-100ns >> > > >> > > Until the cosine content of the first 3 principal components that >> account >> > > for most of the variance in the atomic fluctuation have been dropped at >> > > least once below 0.5. This is the point where theoretically the system >> > has >> > > equilibrated enough. >> > > >> > > Thomas >> > > >> > > >> > > On 22 February 2013 13:43, Ahmet yıldırım <ahmedo...@gmail.com> wrote: >> > > >> > >> Dear users, >> > >> >> > >> I performed MD simulation of 400 ns of a structure. I used the cosine >> > >> content to check whether the simulation is not converged. I used last >> > 100 >> > >> and 50 ns of trajectory to the analysis, respectively. The results >> were >> > >> very similar to each other.The cosine contents of the first ten >> > principal >> > >> components are as follows. The cosine contents of the principal >> > components >> > >> are very small but one. Why is the second cosine content differs from >> > the >> > >> others? What could be the reason for this? And do you think simulation >> > has >> > >> reached convergence? >> > >> >> > >> The cosine contents of last 50 ns: >> > >> 1 0.00685769 >> > >> 2 0.137028 >> > >> 3 0.00139929 >> > >> 4 0.00903137 >> > >> 5 0.0180072 >> > >> 6 0.0128686 >> > >> 7 0.00154502 >> > >> 8 9.71793e-05 >> > >> 9 0.00485945 >> > >> 10 0.00202377 >> > >> >> > >> Thanks in advance >> > >> -- >> > >> Ahmet Yıldırım >> > >> -- >> > >> 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 >> > >> >> > > >> > > >> > > >> > > -- >> > > >> > > ====================================================================== >> > > >> > > Thomas Evangelidis >> > > >> > > PhD student >> > > University of Athens >> > > Faculty of Pharmacy >> > > Department of Pharmaceutical Chemistry >> > > Panepistimioupoli-Zografou >> > > 157 71 Athens >> > > GREECE >> > > >> > > email: tev...@pharm.uoa.gr >> > > >> > > teva...@gmail.com >> > > >> > > >> > > website: https://sites.google.com/site/thomasevangelidishomepage/ >> > > -- >> > > 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 >> > Biocomputing Group >> > Department of Biological Sciences >> > 2500 University Drive NW >> > Calgary, AB T2N 1N4 >> > Canada >> > -- >> > 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 >> > >> >> >> >> -- >> >> ====================================================================== >> >> Thomas Evangelidis >> >> PhD student >> University of Athens >> Faculty of Pharmacy >> Department of Pharmaceutical Chemistry >> Panepistimioupoli-Zografou >> 157 71 Athens >> GREECE >> >> email: tev...@pharm.uoa.gr >> >> teva...@gmail.com >> >> >> website: https://sites.google.com/site/thomasevangelidishomepage/ >> -- >> 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 >> > > > > -- > Ahmet Yıldırım > -- > 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 Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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? 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