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://amber.ch.ic.ac.uk/tutorial/polyA-polyT_New/index.html
http://www.rosswalker.co.uk/movie_sounds/
http://www.rosswalker.co.uk/adsense_alternatives/
http://coffee.sdsc.edu/rcw/tivo_upgrade/
--
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (516) 632-1336
Department of Chemistry Fax: (516) 632-7960
SUNY at Stony Brook Web:
Stony Brook, NY 11794-3400 E-mail: csimmerling_at_sbchem.sunysb.edu
===================================================================
Received on Thu Apr 29 1999 - 10:29:02 PDT
