Hi John,
i think you are referring to 2 different things: the amber *program package*
whose latest version, hopefully shipping today :) , is 7, and, on the other
side the amber *force field*, which gives in different flavors ,i.a., 94, 99,
ff02 ... the issue of removal of translational and rotational motion during a
md simulation (to avoid e.g. the "flying ice cube effect" if you use a water
box) can be solved, as far as i know, already in amber5 or 6. it works through
the sander namelist (ntcm=1, see also the nscm flag). i suggest you to check
the documentation and the amber web site. but don't hesitate to contact me if
you have any other questions.
best regards & happy weekend
felipe
--
Dr. Luis Felipe Pineda De Castro
EnTec GmbH
Structural Bioinformatics and Drug Design
Adolf-Reichwein-Str. 20 Phone: +49-3641-65-6493
D-07745 Jena, Fax: +49-3641-65-8436
GERMANY
e-Mail: pineda_at_imb-jena.de
web : http://www.entec-jena.de
Received on Fri Mar 01 2002 - 00:25:27 PST
