Introduction Statistical mechanics Molecular dynamics Monte Carlo methods Some tricks of the trade How to analyse the results Advanced simulation techniques Non-equilibrium molecular dynamics Brownian dynamics Quantum simulations Some applications Appendix A: Computers and computer simulation Appendix B: Reduced units Appendix C: Calculation of forces and torques Appendix D: Fourier transforms Appendix E: The gear predictor - corrector Appendix F: Programs on microfiche Appendix G: Random numbers References Index.

Computer Simulation of Liquids

http://www2.stat.duke.edu/~scs/Courses/Stat376/Papers/Constraints/Shake1977.pdf

Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes

Liquids exist in a relatively small part of the enormous range of temperatures and pressures existing in the universe. Nevertheless, they are of vital importance for physics and chemistry, for technology, and for life itself. A century of effort since the pioneering work of van der Waals has led to a fairly complete basic understanding of the static and dynamic physicochemical properties of liquids. Advances in statistical mechanics (the fundamental formulations of Gibbs and Boltzmann, integral equations and perturbation theories, computer simulations), in knowledge of intermolecular forces, and in experimental techniques; have all contributed to this. Thirty years ago the very existence of liquids seemed a little mysterious; today one can make fairly precise predictions of the solid-liquid-gas phase diagram and of the microscopic and macroscopic static and dynamic properties of liquids. This paper is a survey, with particular emphasis on equilibrium properties, of the theory which underlies that basic understanding, which is now at least comparable with our understanding of the physics of solids.

What is "liquid"? Understanding the states of matter

The application of the computer simulation method of molecular dynamics to macromolecules is investigated. The protein trypsin inhibitor (BPTI), consisting of 454 united atoms, is used as an example. Different algorithms for integrating the equations of motion are compared, both theoretically and in practice. It is examined to what extent the chain structure of a macromolecule allows a reduction of the computational effort by the introduction of constraints in the dynamics of the chain. A calculational scheme is proposed, by which constraints can be incorporated in predictor-corrector algorithms. The optimum choice of an algorithm depends on the desired accuracy of the solution and on the character of the forces acting on the molecule, viz. whether these are noisy or not. For nonconstraint dynamics a Gear predictor-corrector algorithm yields the best results, whereas for constraint dynamics the Gear and Verlet algorithms produce comparable results. The application of bond-length constraints reduces the re...

Algorithms for macromolecular dynamics and constraint dynamics

During recent decades it has become feasible to simulate the dynamics of molecular systems on a computer. The method of molecular dynamics (MD) solves Newton's equations of motion for a molecular system, which results in trajectories for all atoms in the system. From these atomic trajectories a variety of properties can be calculated. The aim of computer simulations of molecular systems is to compute macroscopic behavior from microscopic interactions. The main contributions a microscopic consideration can offer are (1) the understanding and (2) interpretation of experimental results, (3) semiquantitative estimates of experimental results, and (4) the capability to interpolate or extrapolate experimental data into regions that are only difficultly accessible in the laboratory. One of the two basic problems in the field of molecular modeling and simulation is how to efficiently search the vast configuration space which is spanned by all possible molecular conformations for the global low (free) energy regions which will be populated by a molecular system in thermal equilibrium. The other basic problem is the derivation of a sufficiently accurate interaction energy function or force field for the molecular system of interest. An important part of the art of computer simulation is to choose the unavoidable assumptions, approximations and simplifications of the molecular model and computational procedure such that their contributions to the overall inaccuracy are of comparable size, without affecting significantly the property of interest. Methodology and some practical applications of computer simulation in the field of (bio)chemistry will be reviewed.

Computer-simulation of molecular-dynamics - methodology, applications, and perspectives in chemistry

The molecular-dynamic method was used to simulate a fluid of 500 rigid diatomic homo-nuclear molecules interacting by a double Lennard-Jones potential. The equilibrium and time-dependent properties are calculated in the liquid phase. The computed pressure and the internal energy agree quantitatively to a few percent with experimental values for nitrogen. The reorientational and the velocity of the center-of-gravity self-correlation functions are also discussed. The memory-function formalism and the extended-diffusion models are used to interpret the reorientational self-correlation functions. The analysis reveals that these self-correlation functions have an exponential behavior for times larger than 5 \ifmmode\times\else\texttimes\fi{} 1${0}^{\ensuremath{-}13}$ sec. In this model, considering present computing precision, there is no observable hydrodynamic-type relaxation in the reorientational self-correlation functions.

Simulation of Diatomic Homonuclear Liquids

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Simulation of Diatomic Homonuclear Liquids