AMBER Archive (2006)

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

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Thu May 18 2006 - 00:04:31 CDT

Dear Amber's 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 don't want to constraint water molecules for my MD.

How can I solve this problem ?

Please give me any suggestions.

Thank you.

 

Atsutoshi

 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu