From: Ana Celia Vila Verde (
Date: Tue May 08 2012 - 11:17:41 CDT

Dear Fariba,

I have not used that plugin so I cannot answer your questions,
unfortunately. If you know who wrote the plugin, then I would encourage
you to contact them directly. Even if they do answer, however, you will
still need to /understand/ what the plugin does so you understand what
you are calculating. For that, you really should follow Alex's book
suggestions; you should also download the plugin files and at least get
an idea of what is going on (it might be easier to just write your own
MSD script, though...)

Best of luck,


On 5/8/12 2:06 PM, fariba taghavi wrote:
> Dear vmd users,
> I have some questions about the diffusion coefficient plug-in in VMD.
> 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?
> Any help would be helpful,
> Fariba