Are you looking to have water shown in your average structure? If yes,
averaging may not help since waters exchange locations so you need to
account for that. I would suggest cartesian average on the solute
(appropriately fit to remove translation and rotation) and using a density
contour for solvent. Both can be done in cpptraj. Watch out for internal
dynamics in the solute - it will affect the average, and also may make
interpretation of solvent density difficult. In that case, doing cluster
analysis is probably a better option, and using a cluster representative
rather than average structure. The more flexibility you have in the solute,
the more complex it is to try to show what you're looking for.
On Feb 9, 2015 11:38 AM, "Dr. Robert Molt Jr." <rwmolt07.gmail.com> wrote:
> 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
