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 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
