Re: [AMBER] simulation box shape changed

From: Syed Tarique Moin <>
Date: Thu, 11 Oct 2012 02:10:47 -0700 (PDT)


> From: Jason Swails <>
>To: Syed Tarique Moin <>; AMBER Mailing List <>
>Sent: Thursday, October 4, 2012 1:44 PM
>Subject: Re: [AMBER] simulation box shape changed
>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
>AMBER mailing list
AMBER mailing list
Received on Thu Oct 11 2012 - 02:30:03 PDT
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