The factor of 10 comes from converting the slope (gradient) from A**2/ps to
cm**2/s. The (1/6) factor comes from the definition of diffusion constant,
ie (1/6)*[slope of MSD vs time].
It's up to you what units you want to present your diffusion constant.
Can you tell us more about the log vs log plot approach? You might get smth
out of the intercept, but not from the slope....
George
On Mon, Apr 1, 2013 at 5:21 AM, Vijay Manickam Achari
<vjrajamany.yahoo.com>wrote:
> Dear Sir/Madam,
>
>
> Here I have a question on determining 'diffusion coefficient' from ptraj
> analysis for my bilayer system.
>
> I used ptraj to calculate diffusion and I go four files such that
> fiilename_x.xmgr,
> fiilename_y.xmgr, fiilename_z.xmgr, fiilename_r.xmgr,fiilename_a.xmgr.
>
>
> ACTIONS
>
> 1> DIFFUSION
> Only the average results will be dumped to
> diff-malto-thermo.dat_?.xmgr
> The time between frames in psec is 5.000.
> To calculated diffusion constants, calculate the slope of the
> lines(s)
> and multiply by 10.0/6.0; this will give units of 1x10**-5 cm**2/s
>
> During the run it is stated that, one must multiply with 10/6 to get the
> unit cm**2/s.
>
> In literature it is stated that to calculate the diffusion coefficient,
> one must plot log vs log graph and find the slope (gradient) of the graph.
> And this slope represent diffusion coefficient.
>
> I just want to get some clarification, do I need to times the factor
> (10/6) with the gradient value from log-log plot? Or I only need to
> multiply for the gradient calculated without log-log plot.
> Or is there any other way to to state?
>
>
> Thanks in advance
> Regards
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
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Received on Mon Apr 01 2013 - 07:30:03 PDT
