[gmx-users] g_hbond : normalization autocorrelation function.

[Nilesh Dhumal]

Erik,

I want autocorrelation function without normalization.

Exact value at t=0, t=1 is with normalization.

Nilesh


> Hi Nilesh,
>
> I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What
> normalisation do you expect?
>
> Kind regards,
> Erik
>
> Erik Marklund, PhD
> Postdoctoral Research Fellow
> Fulford JRF, Somerville College
>
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>
>> On 19 Jul 2015, at 04:07, Nilesh Dhumal <ndhumal at andrew.cmu.edu> wrote:
>>
>> Hello,
>>
>> I am calculating autocorrelation function without normalization using
>> g_hbond
>>
>> g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
>> ./test/hbac_3.xvg -num ./test/num_3.xvg
>>
>> The output,  hbac_3.xvg, don't have normalized auto correlation
>> function.
>> Here is initial part
>>
>> @    title "Hydrogen Bond Autocorrelation"
>> @    xaxis  label "Time (ps)"
>> @    yaxis  label "C(t)"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "Ac\sfin sys\v{}\z{}(t)"
>> @ s1 legend "Ac(t)"
>> @ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
>> @ s3 legend "-dAc\sfs\v{}\z{}/dt"
>>         0           1           1  6.67572e-06    0.761129
>>      0.05    0.961928    0.992146        3398    0.401535
>>       0.1    0.959846    0.991717        3496   0.0419408
>>      0.15    0.957734    0.991281        3599   0.0340092
>>       0.2    0.956446    0.991015        3660    0.022918
>>
>>
>> Why is it not normalized ?
>>
>> Thanks,
>>
>> Nilesh
>>
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