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

[Florian Dommert]

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 ? 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
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>   


-- 
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


-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 252 bytes
Desc: OpenPGP digital signature
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080617/9f829fde/attachment.sig>