[gmx-users] Regarding H-bond autocorrelation

[Erik Marklund]

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
> --
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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