AMBER Archive (2003)

Subject: Re: average structure generated by carnal

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Wed Jan 22 2003 - 09:16:53 CST

Hi,
just my two cents:

If molecular motion during the analyzed time-window is
(quasi)-harmonic, then the average structure
will be very close to a sterically possible structure.
Usually, such average structures are closer to
the (experimentally determined) initial structure,
than any individual snapshot (if things go well ;-).
If 'something happens' during the time-window (e.g.
a nucleic acid base pair opens), the average structure
will look peculiar for the atoms involved in the transition.
In this case, averaging does not seem to make too much sense (?).

...This is just my personal view, so take it with a grain of salt.
Regards
Andreas 

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