Re: diffusion coefficient from rmsd

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Aug 27 2008 - 22:39:52 CDT

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.

-- 
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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
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