Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond
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 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 wrote: > > > >> > >> > >>> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal > >>> 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond
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 wrote: > >> >> >>> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal >>> 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond
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 wrote: > > >> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal >> 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond
> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal > 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 listgmx-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 listgmx-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
Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond
On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal 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? -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 listgmx-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
