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The Art of Molecular Dynamics Simulation, Second Edition by D. C. Rapaport

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10

Geometrically constrained molecules

10.1 Introduction

Some internal degrees of freedom are important to molecular motion, while others can be regarded as frozen. Classical mechanics allows geometrical relations between coordinates to be included as holonomic constraints. We have already encountered constraints in connection with non-Newtonian modifications of the dynamical equations (Chapter 6); here the constraints occur in a Newtonian context, so that there is little doubt as to the physical nature of the trajectories.

In this chapter we focus on a class of model where constraints play an important role, namely, the polymer models used for studying alkane chains and more complex molecules, in which a combination of geometrical constraints ...

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