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

[Erik Marklund]

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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