AMBER Archive (2000)

Subject: Re: Empty gap in the watbox at the beginning of MD

From: David Case (case_at_scripps.edu)
Date: Wed Apr 05 2000 - 10:36:29 CDT

On Fri, Mar 31, 2000, Francois Vanelle wrote:

>
> I observe an
> empty gap in the water box from the very beginning of the run.

This is "normal", although probably not optimal. The intent is to avoid
bad initial van der Waals contacts across the box boundary. Equilibration,
as you note, will remove the gaps.

Because of this, be sure to run a "pressure equilibration", so that the
overall density of the system (which is too low at the beginning) can
increase to its proper value.

The current default behavior in LEaP is probably overly conservative.
Future revisions of the code will allow smaller gaps to be constructed.

...good luck....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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