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

From: Jason Swails <>
Date: Mon, 13 Jul 2015 12:04:35 -0400

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 M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jul 13 2015 - 09:30:03 PDT
Custom Search