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

[Justin Lemkul]

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?

-Justin

-- 

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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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