Subject: Re: CCL:average structures

From: Rick Venable <[email-masked]>
Date: Wed, 12 Nov 1997 14:16:14 -0500 (EST)

On Tue, 11 Nov 1997, Josi Santiago Duca wrote:
> I'd like to know which is (are) the criteria to found an average
> structure once a molecular dynamics is run out on a flexible system (for
> instance, a polyethylene chain with 50 ethylene units) starting the MD
> from different seed numbers. If the chain is flexible, a lot of
> different conformations of similar energies can be reached depending on
> their initial random velocities, after e.g. 50 ps. and keeping the
> kinetic energy constant.  Is there any "usual" convention about finding
> an average structure of this set of corformations? 

I think "average" structures can be real trouble, since they don't
represent any *real* structure.  An example is the case of a torsion that
may be changing between 2 states; averaging gives an intermediate torsion
that may be on a torsional barrier, and is clearly not representative of a
dominant conformation.  Instead, I like to use what I've termed a
"typical" structure; it's a real structure from the trajectory that most
resembles (from an RMSD criterion) the average structure.  It avoids the
prblem of creating unlikely conformations as a consequence of averaging. 

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]  |    \  /  |=|    position of the FDA; for that,
http://nmr1.cber.nih.gov/           \/   |=|    see   http://www.fda.gov  )