AMBER Archive (2008)

Subject: Re: AMBER: Problem with evaporating water over longer simulation times

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Wed Nov 12 2008 - 14:56:16 CST

Thank you Thomas and Gustavo.
This does answer my question. It's good to know that the cause is merely
an imaging issue, rather than some sort of inherent simulation problem
(which would have taken a long time to correct).

Thanks

Sasha

steinbrt_at_rci.rutgers.edu wrote:
> Hi,
>
> what you see is probably atoms drifting out of the initial simulation box
> and sander does not automatically image them back in. Your system still
> corresponds to a densely packed waterbox, it's just a visualisation
> artifact stemming from periodic boundary conditions.
>
> If water really were boiling of (say because of a wrongly set
> thermostate), sander would crash with an error about box size changes.
>
> If you use ptraj to image your trajectories back after the MD run, you
> will see that every atom stayed within the initial box. The waters cant
> escape even if they try ;-)
>
> Regards,
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
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