Biomolecules molecular dynamics

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. 

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. 

Listed is a collection of general-purpose molecular dynamics computer simulation packages for the study of molecular systems. The packages include a wide variety of functionalities for the analysis and simulation of biomolecules. In addition, they contain integrated force fields. 

GROMOS A general-purpose molecular dynamics computer simulation package for the study of biomolecules http //igc.ethz.ch/gromos/weicome.htmi GROMACS (GROningen MAchine for Chemical Simulations) http //rugmdO. chem. rug.ni/ gmx/... 

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... 

Hamelberg, D. Mongan, J. McCammon, J.A., Accelerated molecular dynamics a promising and efficient simulation method for biomolecules, 7. Chem. Phys. 2004,120, 11919-11929... 

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

Molecular dynamics (MD) simulation has been broadly used for exploration of structure dynamics of biomolecules, protein/DNA interaction, and the effect of solvent as well as interaction between CNTs and biomolecules. 

The underlying physical principles of NMR have been established and are well understood.8 Applications of both solid- and solution-state NMR spectroscopy can be found in many different disciplines. It is routinely used in structural elucidation of organic and inorganic compounds, polymers, and biomolecules (e.g., proteins, nucleic acids, and carbohydrates). Additionally, NMR can be used to study molecular interactions (e.g., protein-protein and protein-ligand), molecular dynamics, and chemical reactions. It has also been used extensively in medical research and imaging (magnetic resonance imaging). 

Thermal fluctuations are known to affect considerably the structure and other properties of biomolecules [30]. Recently, it was recognized that conformational changes in DNA can produce significant variations in the t-stacking of base pairs and thereby modulate the efficiency of charge transfer [31-33]. Thus, one has to employ a combination of molecular dynamics... 

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,... 

This bimodal dynamics of hydration water is intriguing. A model based on dynamic equilibrium between quasi-bound and free water molecules on the surface of biomolecules (or self-assembly) predicts that the orientational relaxation at a macromolecular surface should indeed be biexponential, with a fast time component (few ps) nearly equal to that of the free water while the long time component is equal to the inverse of the rate of bound to free transition [4], In order to gain an in depth understanding of hydration dynamics, we have carried out detailed atomistic molecular dynamics (MD) simulation studies of water dynamics at the surface of an anionic micelle of cesium perfluorooctanoate (CsPFO), a cationic micelle of cetyl trimethy-lainmonium bromide (CTAB), and also at the surface of a small protein (enterotoxin) using classical, non-polarizable force fields. In particular we have studied the hydrogen bond lifetime dynamics, rotational and dielectric relaxation, translational diffusion and vibrational dynamics of the surface water molecules. In this article we discuss the water dynamics at the surface of CsPFO and of enterotoxin. 

Abstract You can calculate molecular geometries, rates and equilibria, spectra, and other physical properties. The tools of computational chemistry are molecular mechanics, ab initio, semiempirical and density functional methods, and molecular dynamics. Computational chemistry is widely used in the pharmaceutical industry to explore the interactions of potential drugs with biomolecules, for example by docking a candidate drug into the active site of an enzyme. It is also used to investigate the properties of solids (e.g. plastics) in materials science. It does not replace experiment, which remains the final arbiter of truth about Nature. 

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