Molecular dynamics methodology

Gunsteren W F and H J C Berendsen 1990. Computer Simulation of Molecular Dynamics Methodology, Applications and Perspectives in Chemistry. Angewandte Chemie International Edition in English 29 992-1023. 

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. 

Van Gunsteren WF Berendsen HJC. Computer simulation of molecular dynamics methodology, application and perspectives in chemistry. Angew. Chem. Int. Ed. Eng. 1990 29 992-996. 

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 an investigation of the role of water in enzymic catalysis. Brooks and Karplus (1989) chose lysozyme for their study. Stochastic boundary molecular dynamics methodology was applied, with which it was possible to focus on a small part of the overall system (i.e., the active site, substrate, and surrounding solvent). It was shown that both structure and dynamics are affected by solvent. These effects are mediated through solvation of polar residues, as well as stabilization of like-charged ion pairs. Conversely, the effects of the protein on solvent dynamics and... 

Computer Simulation of Molecular Dynamics Methodology, Applications, and Perspectives in Chemistry. 

Liquids are difficult to model computationally because the individual molecules (or ions) that make up the liquid are not isolated (as in the gas phase), but are interacting with each other. These interactions are not symmetric and static (as in solids) but are randomized and dynamic. Thus, errors are introduced when attempts are made to extract a portion of the liquid for study. This problem can be maneuvered around by taking a large portion and by controlling the boundary conditions of the sample. The techniques for extracting a sample and for treating the boundary of a sample are well established within the molecular dynamics methodologies. 

W. F. van Gunsteren and H. J. C. Berendsen, Angew. Chem., Int. Ed. Engl., 29,992 (1990). Computer Simulation of Molecular Dynamics—Methodology, Applications and Perspectives, in Chemistry. 

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