Literature DB >> 15740235

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

Xiongwu Wu1, Bernard R Brooks.   

Abstract

This work presents an accurate and efficient approach to the calculation of long-range interactions for molecular modeling and simulation. This method defines a local region for each particle and describes the remaining region as images of the local region statistically distributed in an isotropic and periodic way, which we call isotropic periodic images. Different from lattice sum methods that sum over discrete lattice images generated by periodic boundary conditions, this method sums over the isotropic periodic images to calculate long-range interactions, and is referred to as the isotropic periodic sum (IPS) method. The IPS method is not a lattice sum method and eliminates the need for a reciprocal space sum. Several analytic solutions of IPS for commonly used potentials are presented. It is demonstrated that the IPS method produces results very similar to that of Ewald summation, but with three major advantages, (1) it eliminates unwanted symmetry artifacts raised from periodic boundary conditions, (2) it can be applied to potentials of any functional form and to fully and partially homogenous systems as well as finite systems, and (3) it is more computationally efficient and can be easily parallelized for multiprocessor computers. Therefore, this method provides a general approach to an efficient calculation of long-range interactions for various kinds of molecular systems. (c) 2005 American Institute of Physics.

Year:  2005        PMID: 15740235      PMCID: PMC6488042          DOI: 10.1063/1.1836733

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


  33 in total

1.  An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

Authors:  Yuchun Lin; Andrij Baumketner; Shaozhong Deng; Zhenli Xu; Donald Jacobs; Wei Cai
Journal:  J Chem Phys       Date:  2009-10-21       Impact factor: 3.488

2.  UNDERSTANDING STRUCTURAL EFFECTS OF MULTIPOLE MOMENTS ON AQUEOUS SOLVATION OF IONS USING THE SOFT-STICKY DIPOLE-QUADRUPOLE-OCTUPOLE WATER MODEL.

Authors:  Jerez A Te; Toshiko Ichiye
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3.  Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction.

Authors:  Lauren Wickstrom; Yuan Bi; Viktor Hornak; Daniel P Raleigh; Carlos Simmerling
Journal:  Biochemistry       Date:  2007-03-06       Impact factor: 3.162

Review 4.  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

5.  Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2008-10-21       Impact factor: 3.488

6.  Interplay of local hydrogen-bonding and long-ranged dipolar forces in simulations of confined water.

Authors:  Jocelyn M Rodgers; John D Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-08       Impact factor: 11.205

Review 7.  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

8.  The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.

Authors:  Jian Yin; Niel M Henriksen; David R Slochower; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2016-09-16       Impact factor: 3.686

9.  Isotropic periodic sum of electrostatic interactions for polar systems.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2009-07-14       Impact factor: 3.488

10.  Molecular modeling of nucleic acid structure: electrostatics and solvation.

Authors:  T E Cheatham; B R Brooks; P A Kollman
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2001-08
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