[gmx-users] g_hbond : normalization autocorrelation function.

[Justin Lemkul]

On 7/19/15 10:55 AM, Nilesh Dhumal wrote:
> Erik,
>
> I want autocorrelation function without normalization.
>

Use the -nonormalize option.

-Justin

> 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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>>
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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================