Re: [AMBER] How to avoid protein drift?

From: Jason Swails <>
Date: Sun, 7 Jun 2015 12:36:51 -0400

On Sun, Jun 7, 2015 at 8:08 AM, Michael Shokhen <>

> Dear Amber List members,
> I have observed that already after 5 ns MD simulation
> a protein molecule is considerably shifted
> towards one of the side of cubic periodic box.
> Obviously that with such a trend after hundreds ns simulations the protein
> will drift out of the periodic box.

> In my simulation I used iwrap=1 that keeps imaging of water molecules
> in frames of periodic box. But how to avoid diffusional drifting of protein
> out of periodic box? I guess there should be a command that keeps the

There is no single definition of the unit cell in a system with periodic
boundary conditions. The unit cell remains valid under any translation,
which means that you can define the unit cell for each frame such that the
center of your solute coincides with the center of the unit cell. Since
the solute is often what you want to analyze or visualize, this is a very
popular choice of unit cell for visualization and analysis. This is what
the "autoimage" command in cpptraj does by default.

If all you are concerned about is visualizing or analyzing the protein in
the center of the unit cell, then you should image the trajectory in that
way, do not try and add any kinds of constraints or restraints to impose
that restriction. This is true of any simulation package (it's a
fundamental concept of periodic boundary conditions).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Jun 07 2015 - 10:00:02 PDT
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