Re: diffusion coefficient from rmsd

From: bo liu (
Date: Thu Aug 28 2008 - 01:38:38 CDT

Agree with Axel,

another approach to get diffusion coefficient would be using Green-Kubo
In this case, you can utilize your Vel.DCD output, then calculate the
Auto-correlation function of COM velocities for the particle.
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 :)

2008/8/28 Axel Kohlmeyer <>

> 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:
> 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:
> 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
> 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
Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
College of Chemistry and Chemical Engineering, Graduate University of
Chinese Academy of Sciences, Beijing P.R. China
Office: (86)-010-88233187
Home: (86)-010-88259765
Cell: 13426057875

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