Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics

From: Zhang, Sixue <>
Date: Thu, 5 Mar 2015 02:44:51 +0000

Hi David,

I used autoimage command in cpptraj, it doesn't bring the box back to the rectangular shape as I defined.

What else wrapping command can I try besides adding iwrap=1 in the input file?



-----Original Message-----
From: David Case []
Sent: Wednesday, March 4, 2015 7:02 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics

> On Mar 4, 2015, at 5:46 PM, Zhang, Sixue <> wrote:
> I brought out an solvent box issue to this mailing list a few weeks ago. I found that the solvent box became very weird in shape after dynamics (NVT or NPT). It looks like the water was boiling.

This *sounds* like something completely normal. Have you used the autoimage command in cpptraj? Does that not help?

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