Re: NTT=5?

From: David Case <>
Date: Tue 30 Apr 2002 11:16:04 -0700

On Tue, Apr 30, 2002, Jung-Hsing Lin wrote:
> I personally feel it is not proper to use the NVE option for long
> simulations, even if numberical errors could be minimal. I guess most
> AMBER users want to simulate at ambient temperatures, so that they can
> compare with experimental results.

There is a large literature on this general subject; here I will just
make two quick comments of my personal views:

(1) many Amber users are interested in dynamical properties of their
systems, for which NVE is the correct approach. All temperature coupling
schemes modify Newton's equations to a greater or lesser extent.

(2) In an NVE simulation of a solvated protein (or DNA), the properties
of the solute (protein) will be close to canonical: the solvent
molecules will provide the "heat bath", and there will be fluctuations in
the internal energy of the protein, as in the canonical ensemble.
[Indeed, analysis of the behavior of a small portion of a larger,
microcanonical, system forms the foundations of our understanding of the
canonical ensemble itself.]

Of course, if you are specifically interested in equilibrium fluctuation
behavior (and not in dynamical behavior), an integration scheme that
guarantees canonical behavior (as in ROAR) might be what you want.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Tue Apr 30 2002 - 11:16:04 PDT
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