AMBER Archive (1999)

Subject: Re: Solvent equilibration problem

From: Carlos Simmerling (carlos_at_poblano.chem.sunysb.edu)
Date: Thu Apr 29 1999 - 12:29:02 CDT

Well if she is trying to equilibrate the box size,
she should use molecule-based pressure scaling (see NPSCAL)
with the belly option. If she uses constant volume the
box will not shrink, she wants to equilibrate the
initial density using constant pressure. With atom-based
scaling, the atoms will be moved even if the belly option
is used. See Tom Cheatham's nice description on the
AMBER web page under the tutorial section:

http://www.amber.ucsf.edu/amber/tutorial/polyA-polyT/index.html 

--
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Carlos L. Simmerling, Ph.D.
Assistant Professor           Phone: (516) 632-1336
Department of Chemistry       Fax:   (516) 632-7960
SUNY at Stony Brook           Web:   http://morita.chem.sunysb.edu/~carlos
Stony Brook, NY 11794-3400    E-mail: csimmerling_at_sbchem.sunysb.edu
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