VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Mar 19 2008 - 06:09:56 CDT

On Wed, 19 Mar 2008, Massimo Lai wrote:

ML> Dear all,

dear massimo,

ML> actually it seems there is material about the link between diffusivity and
ML> equilibrium fluctuations expressed in terms of RMSD, see for example:
ML>
ML> http://www.fisica.uniud.it/~ercolessi/md/md/node36.html#SECTION00556000000000000000

no. this is a misunderstanding that i already suspected in my
first reply. this page refers to "mean squared displacement",
i.e. the average squared distance a particle (or its center of mass)
has passed over time.

the RMSD tool and the RMSD-trajectory tool compute the
"root mean squared deviation" from a reference structure
as a measure of "deformation" of its structure and usually
the translational and rotational displacement is actually
removed before to minimize the RMSD, i.e. to avoid getting
bogus numbers because of translation or rotation.

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

a tool to apply the einstein relation should be rather simple
to implement with scripting, but using the simple displacement
over a trajectory is associated with a significant error so
one frequently computes the MSD for a given time range t0 to t0+tmax
and then moves t0 through the trajectory and finally fits
a straight line to the last part (last third) after checking
its convergence.

cheers,
   axel.

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

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