[gmx-users] mutual diffusion coefficient

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 30 08:55:23 CET 2006

On Sun, 29 Jan 2006, ARGYRIOS KARATRANTOS wrote:

>is there any way in Gromacs to calculate the mutual diffusion coefficient for
>the motion of two particles?
>the mutual diffusion coefficient is defined as the limit as t goes to infinity 
> Dm=lim({[r1(t)-r2(0)]^2}/6t)

What you describe is the self-diffusion which you get from g_msd. Mutual 
diffusion is much more complicated, but there are some recent papers 
describing how to do it. Check literature (Hawlicka), and please implement 
it in g_msd (or in a new program).

Sorry I misread your equation (missed the 1 and 2). Are you sure this is 
the right equation? If so, do you have a reference?

If this is indeed correct, then it shouldn't be very hard to implement in 
g_msd .... Please do it!

>Argyris Karatrantos
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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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