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The Accuracy of Generalized Born Forces

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Computational Electrostatics for Biological Applications

Abstract

Generalized Born (GB) models play an important role in biomolecular dynamics simulations. The issue of the accuracy of solvation forces computed according to these models has not been investigated in much detail to the best of our knowledge. Optimal atomic radii have been derived for most used force fields in order to reproduce molecular dynamics results under the Poisson–Boltzmann (PB) continuum model. In principle, if optimized radii are used, the PB model reproduces well MD simulations. For this reason in this contribution, we consider the most used GB model implementations in publicly available molecular dynamics simulation softwares and assess the accuracy of GB solvation forces compared to the reference PB ones. The results show that current implementations that compute forces by pairwise summations correlate very well with PB forces if judicious choice of model parameters is performed. The latter can be obtained by linear fitting of solvation self-energies computed by the most accurate GBR6 GB model.

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Acknowledgments

This work was partly supported by Ministero dell’Istruzione, dell’Universita’ e della Ricerca (PRIN 2012A7LMS3_001).

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Authors and Affiliations

  1. Dipartimento di Scienze Mediche E Biologiche, Universita’ di Udine, Piazzale Kolbe 4, 33100, Udine, Italy

    Federico Fogolari, Alessandra Corazza & Gennaro Esposito

  2. Istituto Nazionale Biostrutture E Biosistemi, Viale Medaglie D’Oro, 305-00136, Roma, Italy

    Federico Fogolari, Alessandra Corazza & Gennaro Esposito

Authors
  1. Federico Fogolari
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  2. Alessandra Corazza
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  3. Gennaro Esposito
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Corresponding author

Correspondence to Federico Fogolari .

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Editors and Affiliations

  1. CONCEPT Lab - CompuNet, Istituto Italiano di Tecnologia, Genova, Italy

    Walter Rocchia

  2. Institute of Applied Mathematics and Inf, National Research Council, Genova, Italy

    Michela Spagnuolo

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Fogolari, F., Corazza, A., Esposito, G. (2015). The Accuracy of Generalized Born Forces. In: Rocchia, W., Spagnuolo, M. (eds) Computational Electrostatics for Biological Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-12211-3_7

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