Simulating the Dynamics of Macromolecules

  • T. P. Flores
  • D. S. Moss
Chapter
Part of the Topics in Molecular and Structural Biology book series (TMSB)

Abstract

Equilibria in biological systems are governed by their tendency to move towards states of lower free energy. The equilibrium constant K for a chemical reaction at constant temperature and pressure is related to the change in free energy by the equation
$$\Delta G = - RT\ln \;K$$
(1.1)
where G is the Gibbs free energy, R is the gas constant and T is the absolute temperature. The change in G may be related to the changes in the internal energy E, pressure P, volume V and entropy S by the equation
$$\Delta G = \Delta E + P\Delta V - T\Delta S$$
(1.2)
In a well-ordered system at modest temperatures ΔE may dominate this equation and the stable conformation of a molecular system may be calculated by minimizing the internal energy E. This energy is the sum of potential and kinetic energies and, as the latter depends only on temperature, the problem reduces to the minimization of the potential energy. This is discussed in the section entitled Other methods employed in molecular simulations.
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© Macmillan Publishers Limited 1991

Authors and Affiliations

  • T. P. Flores
  • D. S. Moss

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