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

From: David Case <>
Date: Wed 5 Apr 2000 08:36:29 -0700

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:
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:                         
La Jolla CA 92037  USA            |
Received on Wed Apr 05 2000 - 08:36:29 PDT
Custom Search