[gmx-users] g_hbond : normalization autocorrelation function.

[Erik Marklund]

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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