Potentials and Algorithms for Incorporating Polarizability in Computer Simulations

Rick, Steven W.; Stuart, Steven J.

doi:10.1002/0471433519.ch3

Cited by 195 publications

(291 citation statements)

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“…These are total potential energies for the molecule, where backbone dihedral parameters are the adjustable variables in the optimization. For example, if we optimized the absolute difference of QM and MM energies for glycine tetrapeptide (Gly 3 ), we would minimize the absolute error (ae) between the MM and QM energies (Equation 1): (1) where E QM (i) and E MM (i) correspond to the QM and MM energies respectively for i-th glycine tetrapeptide conformer and N is the number of all glycine conformers. In our case, MM energy for a given conformer is given by the AMBER energy function (see ff94 5 ): (2) where the dihedral energy term is: (3) V n is dihedral force constant (amplitude), n is dihedral periodicity, and γ n is a phase of the dihedral angle θ (which would be either φ or ψ for backbone dihedral terms).…”

Section: Optimization Of Backbone Dihedral Parametersmentioning

confidence: 99%

“…The function we used for optimization is somewhat more complicated than that shown in Equation 1. Since the zero of the MM energy function is arbitrary, the optimization should be performed using energy differences between alternate conformations.…”

Section: Optimization Of Backbone Dihedral Parametersmentioning

confidence: 99%

“…In spite of persistent yet slow emergence of force fields that explicitly account for charge polarization 1 , the fixed charge additive force fields remain popular due to computational efficiency. For a more in-depth overview of current force fields and trends in force field development, the reader is referred to recent review articles [2][3][4] .…”

Section: Introductionmentioning

confidence: 99%

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

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The ff94 force field that is commonly associated with the AMBER simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over stabilization of α-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "AMBER" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in AMBER of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab-initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides, and better accord with experimental NMR relaxation data of test protein systems.

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Section: Optimization Of Backbone Dihedral Parametersmentioning

confidence: 99%

Section: Optimization Of Backbone Dihedral Parametersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

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“…8,9 Water has been the focus of many such studies due to its highly polarizable, hydrogen bonded nature, and obvious biological importance.…”

Section: Introductionmentioning

confidence: 99%

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Ren¹,

2003

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A new classical empirical potential is proposed for water. The model uses a polarizable atomic multipole description of electrostatic interactions. Multipoles through the quadrupole are assigned to each atomic center based on a distributed multipole analysis (DMA) derived from large basis set molecular orbital calculations on the water monomer. Polarization is treated via self-consistent induced atomic dipoles. A modified version of Thole's interaction model is used to damp induction at short range. Repulsion-dispersion (vdW) effects are computed from a buffered 14-7 potential. In a departure from most current water potentials, we find that significant vdW parameters are necessary on hydrogen as well as oxygen. The new potential is fully flexible and has been tested versus a variety of experimental data and quantum calculations for small clusters, liquid water, and ice. Overall, excellent agreement with experimental and high level ab initio results is obtained for numerous properties, including cluster structures and energetics and bulk thermodynamic and structural measures. The parametrization scheme described here is easily extended to other molecular systems, and the resulting water potential should provide a useful explicit solvent model for organic solutes and biopolymer modeling. IntroductionEmpirical potential energy functions derived from classical molecular mechanics are central to computational modeling at the atomic level. Molecular mechanics has long enjoyed great success in application to many classes of isolated, gas-phase organic compounds. 1 Beginning with the pioneering work of Bernal and Fowler, 2 water has probably been the target of more potential energy models than any other substance. An interesting overview and historical perspective on the development of water models was recently presented by Finney. 3 Simple nonpolarizable pairwise-additive models that describe the average structure and energetics of liquid water have been in wide use for many years (e.g., TIP3P 4 and SPC 5 ). The recently developed TIP5P potential exhibits excellent agreement with the experimental internal energy, density, and O‚‚‚O radial distribution at room temperature. 6 These models typically use fixed atom-based partial charges to model electrostatics and include polarization response to the environment only in an averaged, mean-field sense. As a result, nonpolarizable potentials that provide excellent descriptions of the homogeneous bulk phase are poor models for gas phase clusters and for nonpolar solutes in polar solvents. For example, the gas phase binding energy of the water dimer is overestimated by more than 30% in the TIP5P model. In application to large biomolecular systems, there is concern that such models cannot correctly account for situations where the same nonpolarizable moiety is exposed to different electrostatic environments, either within a single large static structure or during a course of simulation. In addition, there is an inherent inconsistency in most nonpolarizable models related to thei...

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“…Since nonpolarizable force fields only describe the electrostatic interactions solely in terms of fixed charges [12][13][14], a variety of polarizable force fields, such as AMOEBA [15,16], ABEEM/MM [17] and others [18][19][20], have been proposed including multipole moments and polarization response to the environments.…”

Section: Introductionmentioning

confidence: 99%

Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials

Shen

et al. 2012

J Mol Model

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Coarse-grained studies of CH 3 SH, CH 3 CHO and CHCl 3 liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarsegrained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen.

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Potentials and Algorithms for Incorporating Polarizability in Computer Simulations

Cited by 195 publications

References 0 publications

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials

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