Re: diffusion coefficient from rmsd

From: bo liu (liubo.njuer_at_gmail.com)
Date: Thu Aug 28 2008 - 01:38:38 CDT

Agree with Axel,

another approach to get diffusion coefficient would be using Green-Kubo
relation,
In this case, you can utilize your Vel.DCD output, then calculate the
Auto-correlation function of COM velocities for the particle.
See:
http://www.ks.uiuc.edu/Training/SumSchool/materials/lectures/6-3-Statistical-Mechanics-Proteins/1-ik_diffusion.pdf
though, these two methods(Einstein equation and Green-Kubo relation) focus
on slight differennt dynamic poperties of particles, please refer to
relevant textbooks, a good one could be :Paul Heitjans, J. K., Diffusion in
Condensed Matter. 2005

you can get all the information you need with google :)

Cheers!
2008/8/28 Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>

> On Thu, 28 Aug 2008, Rudra Banerjee wrote:
>
> RB> dear friends,
> RB> how i can calculate diffusion coefficient from rmsd data that we get
> RB> from vmd?
>
> you cannot. an RMSD is a different thing than a MSD.
>
> of course you can script the calculation of the MSD
> in VMD, but you'll have to make sure that your trajectory
> is properly "unwrapped". even more accurate would
> be to compute: d/dt msd(t) for a reasonably long period
> and then average over the horizontal part and then
> apply the einstein relation.
>
> check out slide number 10 of:
> http://www.theochem.rub.de/~axel.kohlmeyer/files/talk-trieste2004-water.pdf
>
> or any decent textbook on theory of liquids.
>
> RB> any idea?
>
> [...]
>
> RB> Please, if possible, don't send me MS Word or PowerPoint
> RB> attachments
> RB> Why?See: http://www.gnu.org/philosophy/no-word-attachments.html
>
> please don't cross-post to multiple mailing lists unless you have
> a very, very, _very_ good reason. not everybody is subscribed to
> all lists... post to one list first and if you don't get a response
> in a reasonable time, try the next.
>
> since you advertise not sending word or powerpoint,
> it would be great if you would also send mails to
> mailing lists only in plain text and _not_ in html.
>
> thanks,
> axel.
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
>
>

-- 
-Liu bo
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Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
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