Literature DB >> 19603970

Isotropic periodic sum of electrostatic interactions for polar systems.

Xiongwu Wu1, Bernard R Brooks.   

Abstract

Isotropic periodic sum (IPS) is a method to calculate long-range interactions based on homogeneity of simulation systems. Long-range interactions are represented by interactions with isotropic periodic images of a defined local region and can be reduced to short ranged IPS potentials. The original electrostatic three-dimensional (3D)-IPS potential was derived based on a nonpolar homogeneous approximation and its application is limited to nonpolar or weak polar systems. This work derived a polar electrostatic 3D-IPS potential based on polar interactions. For the convenience of application, polynomial functions with rationalized coefficients are proposed for electrostatic and Lennard-Jones 3D-IPS potentials. Model systems of various polarities and several commonly used solvent systems are simulated to evaluate the 3D-IPS potentials. It is demonstrated that for polar systems the polar electrostatic 3D-IPS potential has much improved accuracy as compared to the nonpolar 3D-IPS potential. For homogeneous systems, the polar electrostatic 3D-IPS potential with a local region radius or cutoff distance of as small as 10 A can satisfactorily reproduce energetic, structural, and dynamic properties from the particle-meshed-Ewald method. For both homogeneous and heterogeneous systems, the 3D-IPS/discrete fast Fourier transform method using either the nonpolar or the polar electrostatic 3D-IPS potentials results in very similar simulation results.

Entities:  

Mesh:

Substances:

Year:  2009        PMID: 19603970      PMCID: PMC2723922          DOI: 10.1063/1.3160730

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


  14 in total

1.  Dynamical properties of fasciculin-2.

Authors:  N A Baker; V Helms; J A McCammon
Journal:  Proteins       Date:  1999-09-01

Review 2.  Connecting local structure to interface formation: a molecular scale van der Waals theory of nonuniform liquids.

Authors:  John D Weeks
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

3.  Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics.

Authors:  Christopher J Fennell; J Daniel Gezelter
Journal:  J Chem Phys       Date:  2006-06-21       Impact factor: 3.488

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

7.  A new approach for efficient simulation of Coulomb interactions in ionic fluids.

Authors:  Natalia A Denesyuk; John D Weeks
Journal:  J Chem Phys       Date:  2008-03-28       Impact factor: 3.488

8.  Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials.

Authors:  Sergei Izvekov; Jessica M J Swanson; Gregory A Voth
Journal:  J Phys Chem B       Date:  2008-03-27       Impact factor: 2.991

9.  Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.

Authors:  Richard M Venable; Linda E Chen; Richard W Pastor
Journal:  J Phys Chem B       Date:  2009-04-30       Impact factor: 2.991

10.  Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method.

Authors:  Jeffery B Klauda; Xiongwu Wu; Richard W Pastor; Bernard R Brooks
Journal:  J Phys Chem B       Date:  2007-04-11       Impact factor: 2.991

View more
  11 in total

Review 1.  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

2.  The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2019-06-07       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.  Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.

Authors:  Xiongwu Wu; Milan Hodoscek; Bernard R Brooks
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

5.  Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water.

Authors:  Xiongwu Wu; Juyong Lee; Bernard R Brooks
Journal:  J Phys Chem B       Date:  2016-10-18       Impact factor: 2.991

6.  Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps.

Authors:  Xiongwu Wu; Sriram Subramaniam; David A Case; Katherine W Wu; Bernard R Brooks
Journal:  J Struct Biol       Date:  2013-07-20       Impact factor: 2.867

7.  Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations.

Authors:  Pedro Ojeda-May; Jingzhi Pu
Journal:  J Chem Phys       Date:  2015-11-07       Impact factor: 3.488

8.  Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

Authors:  Juyong Lee; Benjamin T Miller; Bernard R Brooks
Journal:  Protein Sci       Date:  2015-08-20       Impact factor: 6.725

9.  Critical test of isotropic periodic sum techniques with group-based cut-off schemes.

Authors:  Takuma Nozawa; Kenji Yasuoka; Kazuaki Z Takahashi
Journal:  Sci Rep       Date:  2018-03-08       Impact factor: 4.379

10.  A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  PLoS Comput Biol       Date:  2015-10-27       Impact factor: 4.475

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.