Molecular dynamics simulation biomolecules

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

Optimized potentials for liquid simulation (OPES) was designed for modeling bulk liquids. It has also seen significant use in modeling the molecular dynamics of biomolecules. OPLS uses five valence terms, one of which is an electrostatic term, but no cross terms. 

In the intervening years, molecular dynamics simulations of biomolecules have undergone an explosive development and been applied to a wide range of problems [3,4]. Two attributes of molecular dynamics simulations have played an essential role in their increasing use. The first is that simulations provide individual particle motions as a function of time so they can answer detailed questions about the properties of a system, often more easily than experiments. For many aspects of biomolecule function, it is these details... 

I am very pleased to have been given the opportunity to contribute a Foreword to this very useful book. It is a particular pleasure for me to do so because all the editors and fifteen of the authors are alumni of my research group at Harvard, where molecular dynamics simulations of biomolecules originated. 

Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD (2006) A polarizable model of water for molecular dynamics simulations of biomolecules. Chem Phys Lett 418(l-3) 245-249... 

Sagui, C. Darden, T., Molecular dynamics simulations of biomolecules long-range electrostatic effects, Ann. Rev. Biophys. Biomol. Struct. 1999, 28, 155-179. 

Cheatham, T. E., IH and Brooks, B. R. 1998. Recent Advances in Molecular Dynamics Simulation Towards the Realistic Representation of Biomolecules in Solution Theor. Chem. Acc., 99, 279. Frenkel, D. and Smit, B. 1996. Understanding Molecular Simulation From Algorithms to Applications,... 

Cheatham TE, Brooks BR (1998) Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution, Theor Chem Acc, 99 279—288... 

Smithrud DB, Wyman TB, Diederich E. Enthalpically driven cyclophane arene inclusion complexation - Solvent-dependent calorimetric studies. J. Am. Chem. Soc. 1991 113 5420-5426. Gilson MK, Zhou HX. Calculation of protein-ligand binding affinities. Annu. Rev. Biophys. Biomol. Struct. 2007 36 21 2. Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002 9 646-652. 

Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 2002 9 646-652. 

Y. Komeiji, M. U. H. Yokoyama, M. Taiji, T. Fukushige, D. Sugimoto, R. Takata, A. Shimizu, and K. Itsukashi, A high performance system for molecular dynamics simulation of biomolecules using special purpose computer, in Proc. of Biocomput., 1996. 

Almond et investigated how aqueous dynamical simulations of flexible molecules can be compared against NMR data. The methodology compares state-of-the-art NMR residual dipolar coupling, NOESY and relaxation, to molecular dynamics simulations in water over several nanoseconds. In contrast to many previous applications of residual dipolar couplings in structure investigation of biomolecules, the approach described here uses MD simulations to provide a dynamic representation of the molecules. 

In the course of this review, we examine how an effective combination of diverse theoretical methods ranging from traditional ab initio, density functional, tight binding, Monte Carlo to molecular dynamics simulations, have helped elucidate the nature of intermolecular interactions in a large number of widely disparate molecular complexes (aqueous and metal clusters, biomolecules), and... 

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