Titlebook: Computer Simulation of Biomolecular Systems; Theoretical and Expe Wilfred F. Gunsteren,Paul K. Weiner,Anthony J. Wil Book 1997 Springer Sci

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A separating framework for increasing the timestep in molecular dynamicsis obtained [1,2]. Typically, . integration algorithms are used: new positions and velocities for all atoms are computed in closed form through simple relations involving positions and velocities at previous steps. Standard explicit schemes are simple to formulate and fast to propagate, but they imp

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Systematic procedure for the development of accurate QM/MM model Hamiltoniansmental chemical reactions that occur in living organisms. Understanding the mechanisms by which enzymes achieve their remarkable catalytic abilities has been a long-standing goal of biochemists, and significant progress has been made since 1878 when Fredrich Wilhelm Kühne first coined the word ‘enzy

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Modeling protonation equilibria in biomoleculesm the normal value, 7.4. It is very unlikely that the effects of abnormal pH result from the destructive chemical action of protons or hydroxide; if this were the case, a blood pH of 6.8, say, would not be dangerous. It is more likely that the sensitivity of organisms to pH results chiefly from the

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Semi-explicit bag model for protein solvationolecules. It is well known that simulations (or free energy calculations) that neglect explicit water are not adequate, while the full inclusion of a large volume of water implies large, if not prohibitive, increases in computational resources [1–5].