[gmx-users] Regarding H-bond autocorrelation

[Erik Marklund]

See the Luzar and chandler papers that I believe are mentioned when you run g_hbond -ac. The subtraction is not mentioned in that paper, however.

Erik

17 jun 2011 kl. 06.59 skrev 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
> 
> 
> 
> -- 
> -----------------------
> 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