AMBER Archive (2009)

Subject: Re: [AMBER] no equilibrium

From: steinbrt_at_rci.rutgers.edu
Date: Mon May 18 2009 - 22:00:40 CDT

Hi,

this sounds as if you didnt wrap your trajectory back into the simulation
box. Amber will not do this automatically, so it may look like your system
blows up. This may be just a visualisation artefact. Use ptraj to make an
imaged trajectory and check if your problem persists.

Kind Regards,

Thomas

On Mon, May 18, 2009 10:44 pm, Nancy wrote:
> Dear all,
>
> I am doing simulation about water conduction through carbon nanotubes
> .Periodic boundary and TIP3P water are used, but no matter how long I
> simulate ,there no equilibrium ,because most water molecules become very
> dispersive and go far away ,even out of sight .I don¡¯t know what is
> wrong ,can anybody give me some advice ?Thanks in advance!
>
> Nancy
>
>
>
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>

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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