Literature DB >> 26814845

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

Christophe Narth1, Louis Lagardère2, Étienne Polack1,3, Nohad Gresh1,4, Qiantao Wang5, David R Bell5, Joshua A Rackers6, Jay W Ponder7, Pengyu Y Ren5, Jean-Philip Piquemal1.   

Abstract

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions.
Copyright © 2016 Wiley Periodicals, Inc.

Entities:  

Keywords:  electrostatics; energy decomposition analysis; polarizable force fields

Mesh:

Substances:

Year:  2016        PMID: 26814845      PMCID: PMC4730919          DOI: 10.1002/jcc.24257

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  32 in total

1.  On the truncation of long-range electrostatic interactions in DNA.

Authors:  J Norberg; L Nilsson
Journal:  Biophys J       Date:  2000-09       Impact factor: 4.033

2.  Benchmarking density functional methods against the S66 and S66x8 datasets for non-covalent interactions.

Authors:  Lars Goerigk; Holger Kruse; Stefan Grimme
Journal:  Chemphyschem       Date:  2011-11-23       Impact factor: 3.102

3.  Toward a Separate Reproduction of the Contributions to the Hartree-Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential.

Authors:  Jean-Philip Piquemal; Hilaire Chevreau; Nohad Gresh
Journal:  J Chem Theory Comput       Date:  2007-05       Impact factor: 6.006

4.  Pair potential for helium from symmetry-adapted perturbation theory calculations and from supermolecular data.

Authors:  Małgorzata Jeziorska; Wojciech Cencek; Konrad Patkowski; Bogumił Jeziorski; Krzysztof Szalewicz
Journal:  J Chem Phys       Date:  2007-09-28       Impact factor: 3.488

Review 5.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

6.  Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding.

Authors:  G A Cisneros; S Na-Im Tholander; O Parisel; T A Darden; D Elking; L Perera; J-P Piquemal
Journal:  Int J Quantum Chem       Date:  2008       Impact factor: 2.444

7.  Origin of the surprising enhancement of electrostatic energies by electron-donating substituents in substituted sandwich benzene dimers.

Authors:  Edward G Hohenstein; Jiana Duan; C David Sherrill
Journal:  J Am Chem Soc       Date:  2011-08-10       Impact factor: 15.419

8.  Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations.

Authors:  Celeste Sagui; Lee G Pedersen; Thomas A Darden
Journal:  J Chem Phys       Date:  2004-01-01       Impact factor: 3.488

9.  S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

Authors:  Robin Chaudret; Nohad Gresh; Christophe Narth; Louis Lagardère; Thomas A Darden; G Andrés Cisneros; Jean-Philip Piquemal
Journal:  J Phys Chem A       Date:  2014-06-19       Impact factor: 2.781

10.  General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field.

Authors:  Qiantao Wang; Joshua A Rackers; Chenfeng He; Rui Qi; Christophe Narth; Louis Lagardere; Nohad Gresh; Jay W Ponder; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2015-04-28       Impact factor: 6.006

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  11 in total

Review 1.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

2.  A physically grounded damped dispersion model with particle mesh Ewald summation.

Authors:  Joshua A Rackers; Chengwen Liu; Pengyu Ren; Jay W Ponder
Journal:  J Chem Phys       Date:  2018-08-28       Impact factor: 3.488

3.  Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.

Authors:  Hao Wang; Weitao Yang
Journal:  J Chem Phys       Date:  2016-06-14       Impact factor: 3.488

4.  Quantum mechanical force fields for condensed phase molecular simulations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Phys Condens Matter       Date:  2017-08-17       Impact factor: 2.333

5.  An optimized charge penetration model for use with the AMOEBA force field.

Authors:  Joshua A Rackers; Qiantao Wang; Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  Phys Chem Chem Phys       Date:  2016-12-21       Impact factor: 3.676

6.  Tinker 8: Software Tools for Molecular Design.

Authors:  Joshua A Rackers; Zhi Wang; Chao Lu; Marie L Laury; Louis Lagardère; Michael J Schnieders; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2018-09-19       Impact factor: 6.006

7.  Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

Authors:  Matthew Harger; Daniel Li; Zhi Wang; Kevin Dalby; Louis Lagardère; Jean-Philip Piquemal; Jay Ponder; Pengyu Ren
Journal:  J Comput Chem       Date:  2017-06-10       Impact factor: 3.376

8.  Polarizable Water Potential Derived from a Model Electron Density.

Authors:  Joshua A Rackers; Roseane R Silva; Zhi Wang; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2021-10-26       Impact factor: 6.006

Review 9.  Advanced Potential Energy Surfaces for Molecular Simulation.

Authors:  Alex Albaugh; Henry A Boateng; Richard T Bradshaw; Omar N Demerdash; Jacek Dziedzic; Yuezhi Mao; Daniel T Margul; Jason Swails; Qiao Zeng; David A Case; Peter Eastman; Lee-Ping Wang; Jonathan W Essex; Martin Head-Gordon; Vijay S Pande; Jay W Ponder; Yihan Shao; Chris-Kriton Skylaris; Ilian T Todorov; Mark E Tuckerman; Teresa Head-Gordon
Journal:  J Phys Chem B       Date:  2016-09-22       Impact factor: 3.466

10.  Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

Authors:  Louis Lagardère; Luc-Henri Jolly; Filippo Lipparini; Félix Aviat; Benjamin Stamm; Zhifeng F Jing; Matthew Harger; Hedieh Torabifard; G Andrés Cisneros; Michael J Schnieders; Nohad Gresh; Yvon Maday; Pengyu Y Ren; Jay W Ponder; Jean-Philip Piquemal
Journal:  Chem Sci       Date:  2017-11-27       Impact factor: 9.825

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