Titlebook: Computational Molecular Dynamics: Challenges, Methods, Ideas; Proceeding of the 2n Peter Deuflhard,Jan Hermans,Robert D. Skeel Conference p

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Scientific Investigations by Supercomputings inside proteins, (2) calculation of binding free energy from “first principles” by a new application of molecular transformation, and (3) extraction of a small ligand (xenon) from a hydrophobic cavity in mutant T4-lysozyme L99A.

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Molecular Dynamics Simulations: The Limits and Beyond is given of methods, algorithms and force fields. After considering the limitations of the standard present-day techniques, developments that reach beyond the present limitations are considered. These concern three major directions: (a) inclusion of quantum dynamics, (b) reduction of complexity by

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Steered Molecular Dynamicscs simulations. Time-dependent external forces are applied to a system, and the responses of the system are analyzed. SMD has already provided important qualitative insights into biologically relevant problems, as demonstrated here for applications ranging from identification of ligand binding pathw

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Conformational Transitions of Proteins from Atomistic Simulationsll loop movements that allow access to the protein’s active site, or large movements such as those of motor proteins that are implicated with muscular extension. Yet, in spite of the increasing number of three-dimensional crystal structures of proteins in different conformations, not much is known a