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      Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

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          Abstract

          Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.

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          Current status of the AMOEBA polarizable force field.

          Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.
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            Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

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              Computing time scales from reaction coordinates by milestoning.

              An algorithm is presented to compute time scales of complex processes following predetermined milestones along a reaction coordinate. A non-Markovian hopping mechanism is assumed and constructed from underlying microscopic dynamics. General analytical analysis, a pedagogical example, and numerical solutions of the non-Markovian model are presented. No assumption is made in the theoretical derivation on the type of microscopic dynamics along the reaction coordinate. However, the detailed calculations are for Brownian dynamics in which the velocities are uncorrelated in time (but spatial memory remains).
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                Author and article information

                Journal
                Annual Review of Biophysics
                Annu. Rev. Biophys.
                Annual Reviews
                1936-122X
                1936-1238
                May 06 2019
                May 06 2019
                : 48
                : 1
                : 371-394
                Affiliations
                [1 ]Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
                [2 ]Sorbonne Université, CNRS, Laboratoire de Chimie Theórique, 75252 Paris CEDEX 05, France
                [3 ]Institut Universitaire de France, 75005 Paris, France
                Article
                10.1146/annurev-biophys-070317-033349
                30916997
                02ebd9a6-64b8-4b97-9928-e72438237c8b
                © 2019
                History

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