[gmx-users] diffusion constant

[David van der Spoel]

On Fri, 6 Aug 2004 parinald at unsl.edu.ar wrote:

>Hello:
>      I try to calculate diffusion constant for Na+ (or Cl-) in water with
>g_msd.
>When I use -mol opcion
>
>          <D> = 0.179 Std. Dev. = 0.000 Error = 0.000
>           D[       Na+] 0.179 (+/- 0.283) 1e-5 cm^2/s
>
>If I not use -mol opcion:
>
>           D[       Na+] 0.330 (+/- 1.489) 1e-5 cm^2/s
>
>Which is the correct value?

The latter. 

The first one gives you the average from the distribution of diffusion 
constants. For very large number of ions and very long sampling the two 
should be much closer, try it for your water molecules.


>                           Thank you.Pablo.
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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