Literature DB >> 23087451

ICSM: An order N method for calculating electrostatic interactions added to TINKER.

Katherine Baker1, Andrij Baumketner, Yuchun Lin, Shaozhong Deng, Donald Jacobs, Wei Cai.   

Abstract

We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, introduced in a previous paper [J. Chem. Phys. 131 (2009) 154103] and termed the Image-Charge Solvation Model (ICSM), is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. A multiple-image method is used to calculate reaction fields due to the implicit part while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the explicit part. The integrated package is validated through test simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system.

Entities:  

Year:  2012        PMID: 23087451      PMCID: PMC3472439          DOI: 10.1016/j.cpc.2012.08.003

Source DB:  PubMed          Journal:  Comput Phys Commun        ISSN: 0010-4655            Impact factor:   4.390


  6 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

Review 2.  Biomolecular modeling: Goals, problems, perspectives.

Authors:  Wilfred F van Gunsteren; Dirk Bakowies; Riccardo Baron; Indira Chandrasekhar; Markus Christen; Xavier Daura; Peter Gee; Daan P Geerke; Alice Glättli; Philippe H Hünenberger; Mika A Kastenholz; Chris Oostenbrink; Merijn Schenk; Daniel Trzesniak; Nico F A van der Vegt; Haibo B Yu
Journal:  Angew Chem Int Ed Engl       Date:  2006-06-19       Impact factor: 15.336

3.  Extending the Fast Multipole Method for Charges inside a Dielectric Sphere in an Ionic Solvent: High Order Image Approximations for Reaction Fields.

Authors:  Shaozhong Deng; Wei Cai
Journal:  J Comput Phys       Date:  2007-12-10       Impact factor: 3.553

4.  Ionic solvation studied by image-charge reaction field method.

Authors:  Yuchun Lin; Andrij Baumketner; Wei Song; Shaozhong Deng; Donald Jacobs; Wei Cai
Journal:  J Chem Phys       Date:  2011-01-28       Impact factor: 3.488

5.  The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm.

Authors:  M E Hodsdon; J W Ponder; D P Cistola
Journal:  J Mol Biol       Date:  1996-12-06       Impact factor: 5.469

6.  Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations.

Authors:  Pengyu Ren; Jay W Ponder
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

  6 in total
  2 in total

1.  Progress in developing Poisson-Boltzmann equation solvers.

Authors:  Chuan Li; Lin Li; Marharyta Petukh; Emil Alexov
Journal:  Mol Based Math Biol       Date:  2013-03-01

2.  Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

Authors:  Shaozhong Deng; Changfeng Xue; Andriy Baumketner; Donald Jacobs; Wei Cai
Journal:  J Comput Phys       Date:  2013-07-01       Impact factor: 3.553

  2 in total

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