Please read about obtaining diffusion constant from VAC in the gromacs wiki.
I wrote an individual article on that topic.
Best,
Vitaly
Subject: RE: [gmx-users] transport properties
> To: Discussion list for GROMACS users <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="utf-8"
>
> Dear K. Chae,
>
> Thank you very much for your answer. I computed velocity auto-correlation
> (VAC) functions , but how can I integrate velocity auto-correlation (VAC)
> functions to get Diffusion coefficient using xmgrace software ? I have just
> used xmgrace to plot md result for analysis. And I have a limited
> information using xmgrace. Could you please explain the integration
> procedure in xmgrace ? I will be very grateful if you can help me to learn
> how to calculate Diffusion coefficient .
>
> Thanks in advance for your helps.
>
> Best regards,
>
> --- On Tue, 4/28/09, kyungchan chae <[email protected]> wrote:
>
>
> From: kyungchan chae <[email protected]>
> Subject: RE: [gmx-users] transport properties
> To: "'Discussion list for GROMACS users'" <[email protected]>
> Date: Tuesday, April 28, 2009, 9:52 AM
>
>
> Once you have correlation results then xmgrace software can do the
> integration.
>
> Regards
>
>
>
> Dear All,
> I'm trying to calculate self diffusion coefficient from velocity
> auto-correlation (VAC) functions using Green-Kubo relation in figure I
> attached to the mail. I couldn’t solve how to integrate the velocity
> auto-correlation (VAC) functions to get Diffusion coefficient. Could you
> please give me some information about this issue ? Could you suggest some
> software to integrate the VAC function ?
> Thanks in advance for your helps.
> Best regards,
>
>
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