Literature DB >> 17973464

Numerical fitting of molecular properties to Hermite Gaussians.

G Andrés Cisneros1, Dennis Elking, Jean-Philip Piquemal, Thomas A Darden.   

Abstract

A procedure is presented to fit gridded molecular properties to auxiliary basis sets (ABSs) of Hermite Gaussians, analogous to the density fitting (DF) method (Dunlap; et al. J. Chem. Phys. 1979, 71, 4993). In this procedure, the ab initio calculated properties (density, electrostatic potential, and/or electric field) are fitted via a linear- or nonlinear-least-squares procedure to auxiliary basis sets (ABS). The calculated fitting coefficients from the numerical grids are shown to be more robust than analytic density fitting due to the neglect of the core contributions. The fitting coefficients are tested by calculating intermolecular Coulomb and exchange interactions for a set of dimers. It is shown that the numerical instabilities observed in DF are caused by the attempt of the ABS to fit the core contributions. In addition, this new approach allows us to reduce the number of functions required to obtain an accurate fit. This results in decreased computational cost, which is shown by calculating the Coulomb energy of a 4096 water box in periodic boundary conditions. Using atom centered Hermite Gaussians, this calculation is only 1 order of magnitude slower than conventional atom-centered point charges.

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Year:  2007        PMID: 17973464      PMCID: PMC2366033          DOI: 10.1021/jp074817r

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  15 in total

1.  Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods.

Authors:  G Andrés Cisneros; Jean-Philip Piquemal; Thomas A Darden
Journal:  J Chem Phys       Date:  2006-11-14       Impact factor: 3.488

2.  The GROMOS software for biomolecular simulation: GROMOS05.

Authors:  Markus Christen; Philippe H Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P Geerke; Tim N Heinz; Mika A Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

3.  GROMACS: fast, flexible, and free.

Authors:  David Van Der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E Mark; Herman J C Berendsen
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

4.  Molecular recognition in organic crystals: directed intermolecular bonds or nonlocalized bonding?

Authors:  Jack D Dunitz; Angelo Gavezzotti
Journal:  Angew Chem Int Ed Engl       Date:  2005-03-11       Impact factor: 15.336

5.  The Amber biomolecular simulation programs.

Authors:  David A Case; Thomas E Cheatham; Tom Darden; Holger Gohlke; Ray Luo; Kenneth M Merz; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J Woods
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

Review 6.  Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

Authors:  William L Jorgensen; Julian Tirado-Rives
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

7.  A CSOV study of the difference between HF and DFT intermolecular interaction energy values: the importance of the charge transfer contribution.

Authors:  Jean-Philip Piquemal; Antonio Marquez; Olivier Parisel; Claude Giessner-Prettre
Journal:  J Comput Chem       Date:  2005-07-30       Impact factor: 3.376

8.  Intermolecular electrostatic energies using density fitting.

Authors:  G Andrés Cisneros; Jean-Philip Piquemal; Thomas A Darden
Journal:  J Chem Phys       Date:  2005-07-22       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.  Towards a force field based on density fitting.

Authors:  Jean-Philip Piquemal; G Andrés Cisneros; Peter Reinhardt; Nohad Gresh; Thomas A Darden
Journal:  J Chem Phys       Date:  2006-03-14       Impact factor: 3.488

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  13 in total

1.  LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Authors:  Eric G Kratz; Alice R Walker; Louis Lagardère; Filippo Lipparini; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Comput Chem       Date:  2016-01-18       Impact factor: 3.376

Review 2.  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

3.  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

4.  Gaussian Multipole Model (GMM).

Authors:  Dennis M Elking; G Andrés Cisneros; Jean-Philip Piquemal; Thomas A Darden; Lee G Pedersen
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

5.  Atomic forces for geometry-dependent point multipole and gaussian multipole models.

Authors:  Dennis M Elking; Lalith Perera; Robert Duke; Thomas Darden; Lee G Pedersen
Journal:  J Comput Chem       Date:  2010-11-30       Impact factor: 3.376

6.  LICHEM 1.1: Recent Improvements and New Capabilities.

Authors:  Hatice Gökcan; Erik Antonio Vázquez-Montelongo; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2019-04-02       Impact factor: 6.006

7.  A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields.

Authors:  Timothy J Giese; Haoyuan Chen; Thakshila Dissanayake; George M Giambaşu; Hugh Heldenbrand; Ming Huang; Erich R Kuechler; Tai-Sung Lee; Maria T Panteva; Brian K Radak; Darrin M York
Journal:  J Chem Theory Comput       Date:  2013-03-12       Impact factor: 6.006

8.  QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential.

Authors:  Hatice Gökcan; Eric Kratz; Thomas A Darden; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Phys Chem Lett       Date:  2018-05-23       Impact factor: 6.475

9.  Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy.

Authors:  Nohad Gresh; G Andrés Cisneros; Thomas A Darden; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2007-11       Impact factor: 6.006

10.  Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM.

Authors:  Robert E Duke; G Andrés Cisneros
Journal:  J Mol Model       Date:  2019-09-09       Impact factor: 1.810

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