Thank you!
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
On 02/09/2015 11:49 AM, Carlos Simmerling wrote:
> 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 - 09:00:05 PST
