[gmx-users] autocorrelation function of hydrogen bond : g_hbond

[Paulo Netz]

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 <ndhumal at 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 <ndhumal at andrew.cmu.edu> wrote:
> >
> >>
> >>
> >>> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
> >>> <ndhumal at 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
> >>>
> >>> ========================================
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