[gmx-users] Regarding H-bond autocorrelation

[bipin singh]

Thanks Sir,for your reply...
I have a silly question regarding the g_hbond's autocorrelation output:
The output contains the following four columns
(i)  Ac fin sys(t)
(ii)  Ac(t)
(iii) Cc contact,hb(t)
(iv) -dAc fs/dt

As I understood the first column is the acf with background
subtraction,and the second column is acf  without
background subtraction.....Can you please refer some text from where I
could get the details about the above
mentioned output options and their importance in in H-bond dynamics.

On Tue, Jun 14, 2011 at 16:53, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> Could be. But, if memory serves me right, there's another dataset in the output, which shows the acf without the "background subtraction".
>
> Erik
>
> 14 jun 2011 kl. 12.10 skrev bipin singh:
>
>> I am using the Gromacs 4.5.3........is  that feature is present in
>> this version......
>>
>> On Mon, Jun 13, 2011 at 21:39, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>>> Hi,
>>>
>>> The problem is that g_hbond subtracts a "background level" to compensate for the finite size of the system. I thought that feature had been taken away, however. Are you using old code?
>>>
>>> Erik
>>>
>>> 12 jun 2011 kl. 19.33 skrev bipin singh:
>>>
>>>> Hello,
>>>>
>>>> I am calculating the H-bond autocorrelation using g_hbond for my
>>>> system, but after plotting
>>>> I have observed that the value for c(t) is reaching to negative, as
>>>> far as I know it can not be
>>>> negative as the probability can not be negative.......please suggest
>>>> where is the problem......
>>>>
>>>> --
>>>> -----------------------
>>>> Thanks and Regards,
>>>> Bipin Singh
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>>>
>>> -----------------------------------------------
>>> Erik Marklund, PhD student
>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>>> phone:    +46 18 471 4537        fax: +46 18 511 755
>>> erikm at xray.bmc.uu.se
>>> http://www2.icm.uu.se/molbio/elflab/index.html
>>>
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>>
>>
>>
>> --
>> -----------------------
>> Regards,
>> Bipin Singh
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
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>
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
> --
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>



-- 
-----------------------
Regards,
Bipin Singh