Molecular dynamics simulation methodology

The primary goal of this appendix is to show how our exposition fits together with the more general MD picture. We feel that this is best done by giving a brief and rather general primer on the basics of Molecular Dynamics simulation methodology. 

Both integral equation and molecular dynamics simulation methodologies have been applied to the question of local solvent structure around solutes in SCFs. These methods incorporate both the direct and indirect mechanisms in an inseparable way however, in molecular dynamics simulation the range of the indirect effects included is limited by the simulation cell size. Probably the first computational observation that the maximum in the local density enhancement (p /p) occurs... 

See van Gunsteren, W.F. Berendsen, H.J.C. Computer simulation of molecular dynamics-methodology, applications, and perspectives in chemistry Angewandre Chemie, International Edition in English, 29 992-1023, 1990, and Karplus, M. Petsko, G.A. Molecular dynamics simulations in biology Nature 347 631-639, 1990. 

Molecular dynamics simulation, which provides the methodology for detailed microscopical modeling on the atomic scale, is a powerful and widely used tool in chemistry, physics, and materials science. This technique is a scheme for the study of the natural time evolution of the system that allows prediction of the static and dynamic properties of substances directly from the underlying interactions between the molecules. 

Baptista M (2002) Comment on Explicit-solvent molecular dynamics simulation at constant pH Methodology and application to small amines . J Chem Phys 116 7766-7768. 

One example of the use of semiempirical methodology is provided in an article detailing a molecular-dynamics simulation of the beta domain of metallothionein with a semiempirical treatment of the metal core.73 The beta domain of rat liver metallothionein-2 contains three-metal centers. In this study, three molecular variants with different metal contents—(1) three cadmium ions, (2) three zinc ions, and (3) one cadmium ion and two zinc ions—were investigated using a conventional molecular dynamics simulation, as well as a simulation with a semiempirical quantum chemical description (MNDO and MNDO/d) of the metal core embedded in a classical environment. For the purely classical simulations, the standard GROMOS96 force-field parameters were used, and parameters were estimated for cadmium. The results of both kinds of simulations were compared to each other... 

The most definitive proof of p-sheet structure requires the determination of the three-dimensional solution structure of the peptide. For the calculation of such structures one requires the accurate determination of coupling constants by DQF-COSY experiments which give backbone dihedral restraints and through-space connectivities (ROESY or NOESY experiments) which give rise to distance restraints. A combination of these restraints allows the calculation of the three-dimensional structure of the peptide using restrained molecular dynamics simulations. Utilizing this methodology, the three-dimensional structures of a number of cyclic peptides have been solved.[411... 

P R E CONTENTS Preface. Stable-Isotope Assisted Protein NMR Spectroscopy in Solution, Brian J. Stockman and John L. Mar-kley. 31P and 1H Two-Dimensional NMR and NOESY-Dis-tance Restrained Molecular Dynamics Methodologies for Defining Sequence-Specific Variations in Duplex Oligonucleotides, David G. Gorenstein, Robert P. Meadows, James T. Metz, Edward Nikonowcz and Carol Beth Post. NMR Study of B- and Z-DNA Hairpins of d[(CG) 3T4(CG)3] in Solution, Sa-toshi Ikuta and Yu-Sen Wang. Molecular Dynamics Simulations of Carbohydrate Molecules, J.W. Brady. Diversity in the Structure of Hemes, Russell Timkovich and Laureano L. Bon-doc. Index. Volume 2,1991, 180 pp. 112.50/E72.50 ISBN 1-55938-396-8... 

In addition to the development in the methodology to compute electronic structures, there have been several attempts to handle the simulation of a chemical event in a system with a large number of degrees of freedom. The Car-Parrinello (CP) approach [5], often referred to as first-principles molecular dynamics (FPMD) method, opened the way to the molecular dynamics simulations based on the first-principles electronic structure calculations. The point of the method is to circumvent the explicit... 

We conclude this section with some brief comments about microscopic dynamics at liquid interfaces. Molecular dynamic simulations of the dynamic properties of liquid interfaces have been limited to the calculation of equilibrium time correlation functions. The methodology of these calculations has been discussed earlier. One property that has received much attention is the molecular reorientation correlation function. If e(r) is a unit vector fixed in the molecular frame, the nth order time correlation function is defined by... 

Molecular dynamics simulation of copper using CHARMM methodological considerations and initial results... 

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