Literature DB >> 24832247

An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald.

Andrew C Simmonett1, Frank C Pickard1, Henry F Schaefer2, Bernard R Brooks1.   

Abstract

Next-generation molecular force fields deliver accurate descriptions of non-covalent interactions by employing more elaborate functional forms than their predecessors. Much work has been dedicated to improving the description of the electrostatic potential (ESP) generated by these force fields. A common approach to improving the ESP is by augmenting the point charges on each center with higher-order multipole moments. The resulting anisotropy greatly improves the directionality of the non-covalent bonding, with a concomitant increase in computational cost. In this work, we develop an efficient strategy for enumerating multipole interactions, by casting an efficient spherical harmonic based approach within a particle mesh Ewald (PME) framework. Although the derivation involves lengthy algebra, the final expressions are relatively compact, yielding an approach that can efficiently handle both finite and periodic systems without imposing any approximations beyond PME. Forces and torques are readily obtained, making our method well suited to modern molecular dynamics simulations.

Mesh:

Year:  2014        PMID: 24832247      PMCID: PMC4032441          DOI: 10.1063/1.4873920

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  17 in total

1.  Notes on "Ewald summation of electrostatic multipole interactions up to quadrupolar level" [J. Chem. Phys. 119, 7471 (2003)].

Authors:  Teodoro Laino; Jürg Hutter
Journal:  J Chem Phys       Date:  2008-08-21       Impact factor: 3.488

Review 2.  Nature and magnitude of aromatic stacking of nucleic acid bases.

Authors:  Jirí Sponer; Kevin E Riley; Pavel Hobza
Journal:  Phys Chem Chem Phys       Date:  2008-04-07       Impact factor: 3.676

3.  Fragmentation methods: a route to accurate calculations on large systems.

Authors:  Mark S Gordon; Dmitri G Fedorov; Spencer R Pruitt; Lyudmila V Slipchenko
Journal:  Chem Rev       Date:  2011-08-26       Impact factor: 60.622

Review 4.  Aromatic-aromatic interaction: a mechanism of protein structure stabilization.

Authors:  S K Burley; G A Petsko
Journal:  Science       Date:  1985-07-05       Impact factor: 47.728

5.  Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility.

Authors:  David S Cerutti; Robert E Duke; Thomas A Darden; Terry P Lybrand
Journal:  J Chem Theory Comput       Date:  2009-09-08       Impact factor: 6.006

Review 6.  Aromatic rings in chemical and biological recognition: energetics and structures.

Authors:  Laura M Salonen; Manuel Ellermann; François Diederich
Journal:  Angew Chem Int Ed Engl       Date:  2011-04-28       Impact factor: 15.336

7.  Aqueous imidazole solutions: a structural perspective from simulations with high-rank electrostatic multipole moments.

Authors:  Steven Y Liem; Majeed S Shaik; Paul L A Popelier
Journal:  J Phys Chem B       Date:  2011-09-09       Impact factor: 2.991

8.  Soft sticky dipole-quadrupole-octupole potential energy function for liquid water: an approximate moment expansion.

Authors:  Toshiko Ichiye; Ming-Liang Tan
Journal:  J Chem Phys       Date:  2006-04-07       Impact factor: 3.488

9.  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

10.  Current and emerging opportunities for molecular simulations in structure-based drug design.

Authors:  Julien Michel
Journal:  Phys Chem Chem Phys       Date:  2014-03-14       Impact factor: 3.676

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  19 in total

1.  Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors.

Authors:  Dejun Lin
Journal:  J Chem Phys       Date:  2015-09-21       Impact factor: 3.488

2.  Efficient treatment of induced dipoles.

Authors:  Andrew C Simmonett; Frank C Pickard; Yihan Shao; Thomas E Cheatham; Bernard R Brooks
Journal:  J Chem Phys       Date:  2015-08-21       Impact factor: 3.488

3.  Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor.

Authors:  Xiongwu Wu; Frank C Pickard; Bernard R Brooks
Journal:  J Chem Phys       Date:  2016-10-28       Impact factor: 3.488

4.  Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Andrew C Simmonett; Florentina Tofoleanu; Juyong Lee; Pavlo O Dral; Samarjeet Prasad; Michael Jones; Yihan Shao; Walter Thiel; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-08-30       Impact factor: 3.686

5.  Understanding how water models affect the anomalous pressure dependence of their diffusion coefficients.

Authors:  Xiaojing Teng; Bailang Liu; Toshiko Ichiye
Journal:  J Chem Phys       Date:  2020-09-14       Impact factor: 3.488

6.  Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Authors:  Jing Huang; Andrew C Simmonett; Frank C Pickard; Alexander D MacKerell; Bernard R Brooks
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

7.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

8.  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

9.  Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2016-05-26       Impact factor: 6.006

10.  Force Fields for Small Molecules.

Authors:  Fang-Yu Lin; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2019
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