> 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