(no subject)

From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Thu Feb 19 2004 - 14:29:21 CST


When you start a simulation or during any given run, you are likely
have a lot
of potential energy which runs down as things evolve. All of this
energy goes
into heating things up. As you said, a simple way to get ride of this
might be to
rescale all of the velocities so that things are at the desired
temperature. But the
question is, is this the best thing to do? We want the dynamics to be
to the underlying physics so another thing to do, is couple the whole
to a larger box in a phenomenological way. this is what langevin
coupling is
doing. it makes sure that you get a boltzmann dist. for your velocities
in the end.

i am not an expert in this by any means, and i hope that i haven't said
incorrect, but all of these kind of questions can easily be answered in
and Smit's Understanding Molecular Simulations, i just don't have it
with me
right now. I suggest this as a starting point; even undergraduates
should be able
to read this book with little trouble.

Michael Grabe, Ph.D.
Post-doctoral Fellow
Howard Hughes Medical Institute
University of California, San Francisco
533 Parnassus Ave.
San Francisco, CA 94143
tel: ++ 415.476.6585

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