Re: [AMBER] unwrap in pytraj?

From: Hai Nguyen <>
Date: Tue, 2 Jul 2019 16:57:52 -0400

On Tue, Jul 2, 2019 at 4:50 PM Shayna Hilburg <>

> Hi all,
> I am trying to do some analysis in python, using coordinates loaded using
> pytraj to find the average frame with mean_structure(traj).
> However, the protein I am analyzing has some atoms that appear far from the
> molecule because of periodic boundary conditions and the simulation had
> iwrap on. Is there a way to move the coordinates so that all bonds are
> unbroken?

> I believe the option is unwrap or autoimage in cpptraj? How do I
> do 'unwrap' in pytraj?

Hi, may be just "traj.autoimage()"?

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Received on Tue Jul 02 2019 - 14:00:03 PDT
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