AMBER Archive (2006)

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

From: german (gsciaini_at_qi.fcen.uba.ar)
Date: Thu May 18 2006 - 07:27:42 CDT

Dear Atsutoshi,

This message means that some part of your simulated system is far away from
the rest, a distance higher than the cutoff. The program uses a virtual box
according to the off value. For instance, a molecule of water could be
evaporated and so it exceeded the virtual box size.

Good Lock...

G.

At 02:04 p.m. 18/05/2006 +0900, you wrote:

>Dear Ambers users,
>
>
>
>I want to simulate in no periodic boundary conditions with explicit water.
>
>So I set ntb=0 in input file following this,
>
>
>
>&cntrl
>
> ntpr=200,ntwx=1000,ntave=1000,
>
> ntb=0, cut=100,
>
> ntf=2, ntc=2,
>
> ntt=1, tautp=0.5, temp0=298.0,
>
> nmropt=1,
>
> nscm=500,
>
> dt=0.002, nstlim=250000,
>
> &end
>
>
>
>But the following error message was output in the end of output file.
>
>
>
>===============================================================================
>
> Frac coord min, max: -1.343330346869949E-004 0.702416488968708
>
> The system has extended beyond
>
>
>
>Does the last error message mean the water surrounding the solute molecule
>splashed outside box ??
>
>But I dont want to constraint water molecules for my MD.
>
>How can I solve this problem ?
>
>Please give me any suggestions.
>
>Thank you.
>
>
>

>
>
>
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