Re: [AMBER] solvent overlap when "iwrap=1"

From: Jason Swails <>
Date: Wed, 1 Dec 2010 09:40:00 -0500

Try setting iwrap to 0, and then reimaging with ptraj. Do you get the same

On Tue, Nov 30, 2010 at 11:58 PM, chicago.ecnu <>wrote:

> Dear Amber users,
> I run MD simulation with "iwrap=1".
> This keyword has the same function as "image" in ptraj.
> However, the structure I got from such simulation seems bad.
> Many solvent molecules were overlapped (One pdb file was attached).
> The MD simulation process works very well, the whole system didn't bomb up.
> Maybe there are some problem in the process of saving coordinate.
> For I want to analyze waters around special amino acids, I want to get the
> real solvent distrubution state from the trajectory.
> Is there any way I can make up?
> I have tried ptraj, but not work.
> Many thanks for your help.
> Yours Sincerely,
> Changge Ji
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Dec 01 2010 - 07:00:06 PST
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