No, this oscillation is related to libration. See, for instance http://www.princeton.edu/~fhs/rahman/rahman.pdf
esp. Fig. 24 in this paper Best regards Paulo Netz On Tue, Apr 9, 2013 at 2:38 PM, Nilesh Dhumal <ndhu...@andrew.cmu.edu>wrote: > Is oscillation is because of change in hydrogen bonded distance? > > Do program consider the change in hydrogen bonded distance during ACF > calculation? > > Nilesh > > > 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 > > > > > -- > 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
