Re: [AMBER] hbond and image problem in cpptraj

From: Daniel Roe <>
Date: Thu, 7 Jan 2016 10:50:45 -0700

On Wed, Jan 6, 2016 at 8:46 PM, Chris <> wrote:
> The result is markedly different only because of the image.
> so,what make me confused is the image. In my option, if trajectory need imaged, it is the same for using 'autoimage' in cpptraj and 'image' in hbond command. Can someone explain such problem.

The only way to detect hydrogen bonds across periodic boundaries is to
use the 'image' keyword with 'hbond'. Otherwise the distances and
angles in the 'hbond' command are calculated without knowledge of the
unit cell. It doesn't matter if you first image the trajectory prior
to 'hbond' if afterwards the hydrogen bond still exists across a
periodic boundary.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jan 07 2016 - 10:00:03 PST
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