From: Axel Kohlmeyer (
Date: Thu Mar 06 2008 - 07:48:05 CST

On Thu, Mar 6, 2008 at 7:45 AM, joy tehrani <> wrote:
> Dear All

dear joy.

> I am interested to use the RMSD trajectory tool and when get the RMSD for
> each frame and save this information as a file.Then I Like to know ,how I
> should calculate the diffusion coeffient for this file and how I can have a

diffusion?? what has root mean squared deviation to do with diffusion?

> plot of time and diffusion coefficient in Excel.

> ps.For ex:I have 40 frames and I ran the simulations for 10000 fs in
> namd.when I want plot the diffusion coefficient with time in a plot ,what
> should I put in the time columns ,before making this chart.

well, just think! you have 40 frames distributed about 10ps? how
far are the individual frames apart. this is the kind of task usually
assigned to children in 3rd or 4th grade...

note bene: 10ps does not give you a lot of accuracy to get
(self-) diffusion. usually several nanoseconds are needed and
even then the error is large.


> Thanks A million
> Joy
> Send instant messages to your online friends

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
If you make something idiot-proof, the universe creates a better idiot.