AMBER Archive (2008)

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

From: steinbrt_at_rci.rutgers.edu
Date: Wed Nov 12 2008 - 13:57:33 CST

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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