Re: [AMBER] Problem in Using the Average Command in Cpptraj

From: Robert Molt <>
Date: Mon, 13 Jul 2015 12:12:38 -0400


On 7/13/15 12:04 PM, Jason Swails wrote:
> On Mon, 2015-07-13 at 11:38 -0400, Robert Molt wrote:
>> Good morning,
>> I am clearly being dense about properly using the average command.
>> For a teaching purpose, I wanted to show a box of water. I created a
>> reasonable equilibrated structure from a truncated octahedral "box"
>> using PBCs. I load the file in cpptraj, specify
>> center :1-550
>> image familiar
> When imaging a trajectory, I recommend *always* using "autoimage"
> instead of those two commands. It will almost always do what you want
> it to do.
>> average Water_550_Average.pdb pdb
> What exactly do you expect this averaging to do? I personally don't
> know what this would even look like, but a sparsely-populated box with
> many overlapping waters is certainly within the realm of expectation.
> Water molecules are constantly exchanging during the course of an MD
> simulation and display a kind of random walk behavior, so an "average"
> position will be rather... strange. As a demonstration, consider two
> interacting water molecules. Now pretend you have two snapshots and the
> only thing different between them is that the two waters have "switched"
> positions. The average structure of those two snapshots will have both
> water molecules superimposed on each other halfway between where each
> was in the two snapshots.
>> The structure I get is a very sparse water box. I obviously am not
>> imaging properly the water molecules from the "center" box (for lack of
>> knowing what to call it). My understanding is that "image" puts all
>> waters in the "center" box, "familiar" is necessary for a truncated
>> octahedron. Is my mistake obvious to anyone?
> If I had to guess, it would be that you are misunderstanding what the
> "average" command is doing here, but without knowing what it is you're
> trying to accomplish, it's just a guess.
> All the best,
> Jason

Dr. Robert Molt Jr.
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Mon Jul 13 2015 - 09:30:04 PDT
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