VMD-L Mailing List

From: Massimo Lai (m.lai_at_cranfield.ac.uk)
Date: Wed Mar 19 2008 - 06:09:44 CDT

Dear all,
actually it seems there is material about the link between diffusivity
and equilibrium fluctuations expressed in terms of RMSD, see for example:

http://www.fisica.uniud.it/~ercolessi/md/md/node36.html#SECTION00556000000000000000

The formulation seems to date back to Einstein's 1905 paper on brownian
motion, so at least in theory it should work. At that point all you need
is a good equilibration I guess... however I haven't tried it myself and
I don't know how the final outcome may look.
I hope this can help.
Cheers
Massimo

Axel Kohlmeyer wrote:
> On Wed, 12 Mar 2008, joy tehrani wrote:
>
> JT> Dear All
>
> dear joy,
>
> JT> I like to know how, I can find the diffusion constant for my
> JT> protein with the results that I got from using the RMSD trajectory
> JT> tool.
>
> as already written before, you cannot. please provide some information
> as to why this should be possible.
>
> cheers,
> axel.
>
> JT>
> JT> Thanks
> JT>
> JT> Joy
> JT>
> JT>
> JT> Send instant messages to your online friends http://uk.messenger.yahoo.com
>
>