Subject: Small Peptide Dynamics

From: [email-masked] (Charles Martin)
Date: Sun, 24 Sep 1995 17:14:28 -0500 (CDT)

Dawei Lin writes..
>
> I want to do molecular dynamics calculation of small peptides(lenght 5 
> to 8). Before I set out to do the calculations, I like to listen any of 
> your suggests or experences. To describe in detail is warmly welcome, 
> such as how many steps will equlibration take, how long time will be 
> enought to get a reasonable structure. The newly references are also welcome.
>I will summary if some thing interesting.

	Some papers by Karl Freed and Graham Flemming at the University of
Chicago discuss this problem. (See, for instance, the special issue of
Chemical Physics on Protein Dynamics Vol 158 (#2,3) 15 December 1991
A paper by Freed and others recently appeared in the Journal of Chemical 
Physics which compares MD simulations on a small peptide with experimental
flouresence depolarization  which measure the orientational
relxation times of the absorbing side group.  The MD simulations fail to
reproduce the experimental relxation time, severely overestimating the 
relaxation time.  

	Given these results, at this point it is unclear to me whether
the potentials used in MD simulations can truly represent the dynamics
of small peptides and proteins.  I have been tracking down
detailed comparisons between MD simulations and dymanics experiments
to answer this.

	I would be most interested in reading other opinions and
seeing other pieces of evidence, pro and/or contrary.  Anyone?

	Chuck Martin

	Theoretical Biophysics 
	The Beckman Institute
	The University of Illionis at Urbana-Champaign