Subject: CCL:average structures

From: Charles & <[email-masked]>
Date: Thu, 13 Nov 1997 13:57:02 -0500

On the topic of average structures for semi-flexible systems

	I would tend to agree with Rick Venable that you can not
really describe a flexible structure (such as a torsional motion or a
semi-flexible polyene chain) using something like an "average
structure."  There are techniques, however, which using averages from
MD simulations to describe such systems, but they require some work
to get at the information you want.

	If you are trying to observe a "floppy" structure, then 
you may wish to condier the type of experiment which probes the
structure.  For example, Karl Freed and Graham Flemming have examined
some cases of flexible amino acid chains in solution and considered
how to explain the experimentally observed flouresence decay
of a TYR group in a floppy environment.  Essentially, one
runs a long time simulation, then  constructs the experimental
time correlation function from a "basis set expansion" of the "space
of correlation functions."  The basis set expansion describes the
chain, essentially, as as a collection of beads of moving under
the influence of random forces, and the correlations which correct
for the non-randomness.   The basis functions are correlation
functions for the EQUILIBRIUM distribution function, and can thus
be obtained from an very good equlibirum simulation.  Using these methods
of non-equlibirum statistical mechanics, one can obtain any
non-equlibirum property, or correlation function,  (i.e. 
like a response to an applied field) by a an expansion in the
basis set of equilibrium correlation functions. (Note that if 
the chain is VERY flexible, then the ends will bump into each other, 
introducing what is termed an excluded volume interaction. 
This complicates the approach described above.)

	Again, this is a non-convetional way of describing "average
strucrues" and is not really available in any standard package.  But perhaps
it will provide some new ways of thinking about the problem.  
Some of the references for this can be found on:

	http://rainbow.uchicago.edu/~freed.html

	With Best Regards
	Chuck Martin

-- 
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Dr. Charles H. Martin
Quantum Theory Project
362 Williamson Hall
PO Box 118435
University of Florida
Gainesville, Florida  32611-8435

Fax: (352) 392-8722
Email: [email-masked]
Web:   www.cat.syr.edu/~cmartin/hv
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