Re: [AMBER] water box corrupted by minimization

From: Michael Shokhen <>
Date: Sat, 6 Nov 2021 16:18:28 +0000

Dear Prof. Case,
Thank you for your response on my report
about the corrupted periodic water box.
You addressed me to the analogous error report from October 6-th
where Prof. Cheatham suggested that it is “likely just an artifact of
the visualization.”
I have identified that the error source is the command “autoimage origin”
in the file:
parm ../mc.prmtop
trajin mdcrd 700000 700000
autoimage origin
trajout heat.pdb pdb
The autoimage origin command must be deleted there.
See the attached figure for illustration.

From: David A Case <>
Sent: Friday, November 5, 2021 3:30 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] water box corrupted by minimization

On Thu, Nov 04, 2021, Michael Shokhen wrote:
>The periodic water box is corrupted by minimization procedure.
>See scripts and figures below.
>I need your advice how to resolve the problem.

Here is a similar report:;;sdata=PhqZffoD83nWbPe1yNrpYfGc%2FFUIJTP48ecTeSyVxjM%3D&amp;reserved=0

Tom lists some ideas for exploring what is going on, and suspects that it is
"just" a visualization artifact. It's not clear that the original poster
last month ever supplied any files that would allow one to reproduce the
problem, so if you could do that, it would probably help.


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Received on Sat Nov 06 2021 - 09:30:02 PDT
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