There's a known oscillation in the ACF that occurs at ~100 fs or so. Is that what you see?
Erik On 9 Apr 2013, at 18:02, Nilesh Dhumal <ndhu...@andrew.cmu.edu> wrote: > > >> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal >> <ndhu...@andrew.cmu.edu>wrote: >> >>> Hello, >>> >>> I am calculating the hydrogen bond autocorrelation function using >>> g_hbond >>> for O-H---O hydrogen bond in system. >>> >>> I made two groups 1. O-H atoms numbers 2. two oxygen atoms are >>> interacting >>> with OH bond. >>> >>> I am using default hydrogen bond criteria (donor-acceptor distance 3.5 >>> and >>> angle 30) for calculating the autocorrelation function. >>> >>> I am not getting a smooth exponential plot. I get a small bump in the >>> plot. >>> >>> Attached the autocorrelation plot. >>> >>> >> Attachments are not allowed on this list. Please provide a link to the >> image. >> >> >>> Why there is not smooth exponential plot. >>> >> >> There is no way to tell, and even with the image there is still no way to >> tell. How much sampling do you have? Have you looked at overall >> convergence, etc? > > > I saved the trajectory at 3fs. > > It converged. > > Nilesh > > > > >> >> -Justin >> >> -- >> >> ======================================== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) >> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> 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 >> > > > -- > 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 -- 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
