Re: [AMBER] simulation box shape changed

From: Jason Swails <>
Date: Thu, 4 Oct 2012 07:44:00 -0400

On Thu, Oct 4, 2012 at 2:46 AM, Syed Tarique Moin <>wrote:

> Hello,
> I am simulating a very small complex (of few atoms) in a water box made
> using solvateoct command. During simulation, water is dispersed out of the
> box. Is there something wrong during my simulation as I have used the
> following protocols..

Why do you not expect this? Water should diffuse naturally, and should
'leave' the simulation box. Remember that these simulations are fully
periodic, though, and each atom appears in every unit cell expanded
infinitely in every direction. Therefore, as soon as one water molecule
exits the unit cell you are 'watching', one of its images enters the cell
on the other side. While the coordinates are only tracked for a single
periodic cell, the simulation includes the effects from all images in all
cells. (Look up the "minimum image convention" in relation to periodic

You can use the "autoimage" command from cpptraj in order to reimage all
atoms back into the same unit cell centered around your solute.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Oct 04 2012 - 05:00:03 PDT
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