AMBER Archive (2002)

Subject: Re: NTT=5?

From: David Case (case_at_scripps.edu)
Date: Tue Apr 30 2002 - 13:16:04 CDT

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.

....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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