AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8

From: Ricardo J. F. Branco <>
Date: Fri, 23 Jun 2006 08:36:44 +0100

Dear AMBER users,

I am using a truncated octehedral TIP3P type water box in my simulations using
PMEMD with AMBER8, however when I try to center and reimage the system using
the common keywords:

center mass
image center

I got a new trajectory with a distorted cubic shape in which the solute is
partialy out of the box and not in the center as I expected!

What should I do to overcome this problem?

Thanks in advance,


 Ricardo J. F. Branco, Ph.D. Student
 Theoretical and Computational Chemistry Group
 REQUIMTE - Faculty of Science
 University of Oporto
 Rua do Campo Alegre, 687
 P 4169-007 Porto, Portugal
 Phone: (+351) 226 082 826
 Fax:   (+351) 226 082 959
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Received on Sun Jun 25 2006 - 06:07:16 PDT
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