AMBER Archive (2005)

Subject: Re: AMBER: solvate water box

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 14 2005 - 11:30:11 CDT

On Wed, Apr 13, 2005, bybaker_at_itsa.ucsf.edu wrote:
>
> I notice that the water molecules were spread at the
> edges and the box was no longer rectangular after the equilibrations.

You need to "re-image" the coordinates back into the central box. See the
"image" command in ptraj.

...dac

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