AMBER Archive (2005)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Mar 31 2005 - 06:26:21 CST

Dear Mr. Case,

Thanks for the suggestion. After setting nscm = 500 (before it was 1000)
the system did not give any error for 200 ps simulation.

Best,

On Wed, 30 Mar 2005, David A. Case wrote:

> 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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-- 
  Ilyas Yildirim
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