Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration

From: <>
Date: Thu, 8 Jul 2010 04:53:53 -0400 (EDT)


as the tutorial states:

- 50 ps of density equilibration (equilibrating T and &#948; at the same
time is not very good form, but we'll get away with it here)

all in one equilibration may lead to problems and I dont recommend it for
actual production runs, but most of the time it should work ok.

Also note the disclaimer on the website ;-)

"These tutorials are meant to provide illustrative examples of how to use
the AMBER software suite to carry out simulations that can be run on a
simple workstation in a reasonable period of time. They do not necessarily
provide the optimal choice of parameters or methods for the particular
application area."


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Jul 08 2010 - 02:00:04 PDT
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