AMBER Archive (2005)

Subject: Re: AMBER: "The system has extended beyond" error

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 30 2005 - 09:08:07 CST

On Tue, Mar 29, 2005, Ilyas Yildirim wrote:
>
> As far as I understand, the above error is saying that the molecule is out
> of the virtual box sander has created.

You should visually look at your trajectory to see what is happening. The
most likely fix is probably to set the nscm parameter to prevent center of
mass translation. But it is also possible that you molecule is flying apart
into to pieces.

...dac

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