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
