AMBER Archive (2006)

Subject: Re: AMBER: Periodic boundary condition (PBC)

From: David A. Case (
Date: Mon Aug 28 2006 - 19:17:42 CDT

On Mon, Aug 28, 2006, Rahaman, Asif wrote:

> I have minimized the system with PBC - It looks fine as structures holds up
> as expected. Then I have heated the system to 30 K with a NVT run. Then I
> see atoms are flying all over as if there in no PBC.

Certainly the thing to check first is if you imaged the system (using the image
command in ptraj), before visualizing it. This is usually the problem when
energies look OK but the box looks visually weird.


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