From: Axel Kohlmeyer (
Date: Tue May 08 2012 - 08:12:35 CDT

On Tue, May 8, 2012 at 8:06 AM, fariba taghavi
<> wrote:
> Dear vmd users,
> I have some questions about the diffusion coefficient plug-in in VMD.

which plugin exactly are you referring to?
there is no such plugin bundled with VMD.
have you checked who is the author of the
plugin and contacted this person?

> I do not know exactly the meaning of "lag times" and "analysis interval" and
> their differences in this plug-in.
> Why analysis interval should be bigger than time lag?
> What is the "premature conclusions"?
> What does a "subsection of the trajectory" mean in "Analysis interval
> boxes"?
> Would you please explain me or introduce me a book or paper about these
> concepts?

this sounds like you need to learn some rather
fundamental concepts of analysis of MD data.
this is handled by any good text book on MD.
try "understanding molecular simulations" by
daan frenkel and berend smit, or if you like it
more technical and "old fashioned" check out
"computer simulations of liquids" by allen and


> Any help would be helpful,
> Fariba

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.