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
