Then, these cosine content's results are all normal? 2013/2/25 Tsjerk Wassenaar <[email protected]>
> 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 <[email protected]> > 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 <[email protected]> > > > >> On 25 February 2013 12:14, Tsjerk Wassenaar <[email protected]> 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 < > [email protected]> > >> > 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 <[email protected]> > 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 [email protected] > >> > >> 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 [email protected]. > >> > >> * 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: [email protected] > >> > > > >> > > [email protected] > >> > > > >> > > > >> > > website: https://sites.google.com/site/thomasevangelidishomepage/ > >> > > -- > >> > > gmx-users mailing list [email protected] > >> > > 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 [email protected]. > >> > > * 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 [email protected] > >> > 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 [email protected]. > >> > * 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: [email protected] > >> > >> [email protected] > >> > >> > >> website: https://sites.google.com/site/thomasevangelidishomepage/ > >> -- > >> gmx-users mailing list [email protected] > >> 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 [email protected]. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > > > > -- > > Ahmet Yıldırım > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > * 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet Yıldırım -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
