I can imagine writing an elaborate script to do the following, but I am
seeking to clarify if there is a simple way to do this in cpptraj, given
its power (I am a new user, and therefore ignorant).
I would like to generate an average structure for an explicit solvent
simulation. Using cpptraj, one can use the average command over an
entire simulation of the Cartesian coordinates. However, I end up having
lots of solvent molecules ontop of each other (which makes sense to me,
that a straight Cartesian average for molecules with lots of drift will
give meaningless results for this reason).
Is it possible to take an average based on internal coordinates? i.e.,
relative distances?
No luck in doing a google search on this one (then again, maybe
"internal coordinates" is the wrong vernacular choice for what I am
looking for?)
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
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Received on Mon Feb 09 2015 - 09:00:04 PST
