Re: AMBER: Periodic boundary condition (PBC)

From: David A. Case <>
Date: Mon, 28 Aug 2006 17:17:42 -0700

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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Received on Wed Aug 30 2006 - 06:07:12 PDT
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