AMBER Archive (2004)

Subject: Re: AMBER: SANDER general questions.

From: Scott Brozell (
Date: Mon Mar 22 2004 - 15:26:55 CST


On Mon, 22 Mar 2004, Osman Gani wrote:

> In the SANDER module (amber 7, page 94), it is said that, setting NTT=0 correspods to microcanonical ensemble; the other options don't correspond to common ensembles. Some aspects of the "weak-coupling ensemble" (NTT=1) have been examined, and rougly interpolate between microcanonical and canonical ensembles.
> My questions are:
> 1)what are meant by canonical and microcanonical ensembles?

You need to study Statistical Mechanics.
Most undergraduate Physical Chemistry textbooks give a simple introduction.
Common graduate texts are by McQuarrie for chemistry and Pathria for physics.
Some aimed at computational science are

%A D. Frenkel
%A B. Smit
%T Understanding Molecular Simulation: From Algorithms to Applications
%I Academic Press
%C San Diego
%D 1996

%A A.R. Leach
%T Molecular Modelling. Principles and Applications, Second Edition
%I Prentice-Hall
%C Harlow, England
%D 2001
%K book

> 2) what is meant by weak-coupling ensemble?

After the above studying read reference 50.

Scott Brozell

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