[gmx-users] Re[4]: g_msd vs g_velacc. [SOLVED]

[Florian Dommert]

Florian Dommert wrote:

> Vitaly Chaban wrote:
>
>   
>>> I've got a discrepancy calculating the diffusion coefficient via
>>> Green-Kubo equation and via Einstein equation.
>>>     
>>>       
>>   
>>     
>>> $ g_velacc -nonormalize -acflen 1001
>>> $ g_analyze -f vac.xvg -integrate
>>> Do I miss any important keyword here? It seems the result of integration is not
>>> correct in this case.
>>>     
>>>       
>> For the VACF of the molecules:
>> $ g_velacc -nonormalize -acflen 1001 -mol -n index.ndx (index.ndx
>> contains the number of molecules for the calculation)
>>
>> $ g_analyze -f vac.xvg -integrate
>>
>> The result should be finally divided by 3.
>>
>>   
>>     
> Hello,
>
>  why should one use a prefactor of 1.0/3.0 ? 
Hi,

 after inspecting a suitable paper (
http://prola.aps.org/abstract/PRA/v11/i6/p2111_1), I got
the prefactor. Sorry for the confusion.

Best Regards

Flo



> I thought the flag -mol
> calculates
> the momentum autocorrelation function, so in my opinion the result has
> to be divided
> by the square of the masses of the molecules to obtain the diffusion
> constant.
>
> Best Regards,
>
>  Flo
>
>
>   
>> --
>> Vitaly V. Chaban
>> School of Chemistry
>> University of Kharkiv
>> Svobody sq.,4
>> Kharkiv 61077, Ukraine
>>
>>
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>>   
>>     
>
>
>   
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-- 
Florian Dommert
Dipl.-Phys.

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert


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