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
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | WWW:
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Received on Wed Apr 05 2000 - 08:36:29 PDT
