Literature DB >> 33722046

Analytical Hessians for Ewald and particle mesh Ewald electrostatics.

Andrew C Simmonett1, Bernard R Brooks1.   

Abstract

The particle mesh Ewald (PME) method has become ubiquitous in the molecular simulation community due to its ability to deliver long range electrostatics accurately with ON  ⁡log(N) complexity. Despite this widespread use, spanning more than two decades, second derivatives (Hessians) have not been available. In this work, we describe the theory and implementation of PME Hessians, which have applications in normal mode analysis, characterization of stationary points, phonon dispersion curve calculation, crystal structure prediction, and efficient geometry optimization. We outline an exact strategy that requires O(1) effort for each Hessian element; after discussing the excessive memory requirements of such an approach, we develop an accurate, efficient approximation that is far more tractable on commodity hardware.

Entities:  

Year:  2021        PMID: 33722046      PMCID: PMC8064412          DOI: 10.1063/5.0044166

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


  16 in total

1.  Isotropic periodic sum: a method for the calculation of long-range interactions.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2005-01-22       Impact factor: 3.488

Review 2.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

3.  Minimax approximation for the decomposition of energy denominators in Laplace-transformed Møller-Plesset perturbation theories.

Authors:  Akio Takatsuka; Seiichiro Ten-No; Wolfgang Hackbusch
Journal:  J Chem Phys       Date:  2008-07-28       Impact factor: 3.488

Review 4.  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

5.  Optical measurements of long-range protein vibrations.

Authors:  Gheorghe Acbas; Katherine A Niessen; Edward H Snell; A G Markelz
Journal:  Nat Commun       Date:  2014       Impact factor: 14.919

6.  Communication: on the origin of the surface term in the Ewald formula.

Authors:  V Ballenegger
Journal:  J Chem Phys       Date:  2014-04-28       Impact factor: 3.488

7.  The u-series: A separable decomposition for electrostatics computation with improved accuracy.

Authors:  Cristian Predescu; Adam K Lerer; Ross A Lippert; Brian Towles; J P Grossman; Robert M Dirks; David E Shaw
Journal:  J Chem Phys       Date:  2020-02-28       Impact factor: 3.488

8.  An Improved Isotropic Periodic Sum Method That Uses Linear Combinations of Basis Potentials.

Authors:  Kazuaki Z Takahashi; Tetsu Narumi; Donguk Suh; Kenji Yasuoka
Journal:  J Chem Theory Comput       Date:  2012-09-27       Impact factor: 6.006

9.  Geometry optimization made simple with translation and rotation coordinates.

Authors:  Lee-Ping Wang; Chenchen Song
Journal:  J Chem Phys       Date:  2016-06-07       Impact factor: 4.304

10.  Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.

Authors:  Stefano Piana; Kresten Lindorff-Larsen; Robert M Dirks; John K Salmon; Ron O Dror; David E Shaw
Journal:  PLoS One       Date:  2012-06-29       Impact factor: 3.240

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