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

[Nilesh Dhumal]

> 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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