Subject: Stochastic dynamics & "reduced atoms"

From: [email-masked] (Gabriel Berriz)
Date: Wed, 21 May 1997 17:35:42 -0400

Dear Netters:

I am a graduate student in biophysics interested in reading about the
use of "reduced atom" or ("reduced molecule") representations(*) in
stochastic dynamics simulations, and in particular, any discussion on
dealing with the distortions in conformational sampling produced by
reduced representations.  (Can one improve the quality of the sampling
in a reduced representation model by modifying the statistical
features of the noise term in the classical Langevin equation?)

I would appreciate your suggestions for readings on this subject.

Thank you very much,

G. Berriz
[email-masked]

(*) P.S. Just in case my terminology is not entirely correct or
standard, I will spell out in more detail what I mean.  I would like
to (eventually) perform stochastic dynamics simulations of long
(model) polymer chains.  Since I am interested in long time scales, I
must keep the molecules' representation, as well as the mechanism for
simulating the stochastic component of the dynamics, as simple as
possible.  For this reason, I would like to use some form of "reduced
atom" representation.  For example, instead of representing a methyl
group by its carbon and three attached hydrogens, one can represent
the whole group by a heavier mass concentrated at their center of
mass.  Alternatively, one can keep all four atoms, but instead of
applying random forces to all of them (this representing the noise
term of the stochastic equation of motion), one could apply only a
random torque around the bond connecting the methyl group to the rest
of the molecule (and treat the rest of the methyl group as rigid).
Another common "reduced atom" representation is the C-alpha-C-alpha
pseudo-bond representation of proteins proposed many years ago by
Flory.  One possible objection to these reduced representations is
that their sampling of conformational space does not correspond
sufficiently closely to the sampling performed by the fully
represented molecule.  As a trivial example of this, the reduced
pseudo-bond representation of a tripeptide, where only the C-alpha
carbons are moved randomly (subject only pseudo-bond length
constraints), allows a considerably greater range for the
C-alpha-C-alpha-C-alpha angle, than does the full representation of
the tripeptide (with its corresponding constraints).