Re: [AMBER] The protein is Leaving the water box!

From: Jason Swails <>
Date: Fri, 14 Aug 2015 09:00:11 -0400

On Fri, Aug 14, 2015 at 8:11 AM, Amber mail <> wrote:

> Thanks a lot for your help !
> So you advice me to continue the simulation.
> By the way, I've just finished another 10 ns of MD production, and attached
> below is a screen shot of the water box after 30 ns MD production
> I don't know why this gap on the right side of the water box was created..?

‚ÄčThis is, again, the effect of periodic boundary conditions. Half of the
protein is sticking out of one side of the unit cell into the adjacent
one. Which means that its periodic image has half of *its* protein
sticking into *that* unit cell.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 14 2015 - 06:30:03 PDT
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