Subject: A question

From: Richard Wood <[email-masked]>
Date: Wed, 26 May 1999 10:04:26 +36000

Hi all on the CCL
   I have a question for you.  I have run 16 molecular dynamics 
simulations of the same molecule, each one using a different set of 
initial velocities.  From these MD simulations, I have calculated various 
properties and obtained their averages.  I have found the lowest PE for 
each MD sim and the corresponding conformation.  My question is this: is 
there any way that I can generate an "average" conformation that would 
give me these "average" properties?

I will post all replies.

Richard

---

From: Peter Shenkin <[email-masked]>
Date: Wed, 26 May 1999 14:24:21 -0400 (EDT)

Hi,

You could get the "average" conformation by doing an rms superposition
of all conformations on the first and averaging coordinates, or by
doing a more sophisticated multiconformer superposition and then
averaging coordinates.  Simon Kearsley has published a multiple
conformation superposition method.  So have we, in our XCluster
paper (J. Comp. Chem., v15, pp899-916, 1994).  Ours involves looking
at all pairwise superpositions.

However you do the superposition, the "average" conformation, defined
as above, might not be terribly useful.  For instance, if half the
conformations have a +60-degree torsion and the other half have a
-60-degree torsion, the average might have a 0-degree torsion, and
thus would not resemble any conformation in the ensemble.  OTOH,
this might be what you want for some applications.

It is sometimes more useful to use the "most representative" structure;
this is the actual structure from the data set that has the smallest
rms interatomic displacement from the average structure.  It's like
using the number from a list of numbers which is closest to the
average, rather than using the average itself.

In XCluster, we first try to find meaningful clusters (maybe there
would be two, one with the +60 and one with the -60 torsion). Then
we write out the the most representative structure from each
cluster.  Or we can write out the average structure, if that's
what you really want.

Hope this helps,
-P.

On Wed, 26 May 1999, Richard Wood wrote:

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