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
