Literature DB >> 22712654

Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

Jun Wang1, Piotr Cieplak, Qin Cai, Meng-Juei Hsieh, Junmei Wang, Yong Duan, Ray Luo.   

Abstract

As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations.

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Year:  2012        PMID: 22712654      PMCID: PMC3493849          DOI: 10.1021/jp212117d

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  9 in total

1.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Authors:  Hans W Horn; William C Swope; Jed W Pitera; Jeffry D Madura; Thomas J Dick; Greg L Hura; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2004-05-22       Impact factor: 3.488

2.  A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums.

Authors:  Steven W Rick
Journal:  J Chem Phys       Date:  2004-04-01       Impact factor: 3.488

3.  Charge-on-spring polarizable water models revisited: from water clusters to liquid water to ice.

Authors:  Haibo Yu; Wilfred F van Gunsteren
Journal:  J Chem Phys       Date:  2004-11-15       Impact factor: 3.488

4.  Polarizable interaction potential for water from coupled cluster calculations. I. Analysis of dimer potential energy surface.

Authors:  Robert Bukowski; Krzysztof Szalewicz; Gerrit C Groenenboom; Ad van der Avoird
Journal:  J Chem Phys       Date:  2008-03-07       Impact factor: 3.488

5.  Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D.

Authors:  Anna-Pitschna E Kunz; Wilfred F van Gunsteren
Journal:  J Phys Chem A       Date:  2009-10-29       Impact factor: 2.781

6.  Polarization effects in molecular mechanical force fields.

Authors:  Piotr Cieplak; François-Yves Dupradeau; Yong Duan; Junmei Wang
Journal:  J Phys Condens Matter       Date:  2009-07-24       Impact factor: 2.333

7.  Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability.

Authors:  Junmei Wang; Piotr Cieplak; Jie Li; Tingjun Hou; Ray Luo; Yong Duan
Journal:  J Phys Chem B       Date:  2011-03-10       Impact factor: 2.991

8.  Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies.

Authors:  Junmei Wang; Piotr Cieplak; Jie Li; Jun Wang; Qin Cai; MengJuei Hsieh; Hongxing Lei; Ray Luo; Yong Duan
Journal:  J Phys Chem B       Date:  2011-03-10       Impact factor: 2.991

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

  9 in total
  20 in total

1.  Matching of additive and polarizable force fields for multiscale condensed phase simulations.

Authors:  Christopher M Baker; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

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.  Quantum mechanical force field for water with explicit electronic polarization.

Authors:  Jaebeom Han; Michael J M Mazack; Peng Zhang; Donald G Truhlar; Jiali Gao
Journal:  J Chem Phys       Date:  2013-08-07       Impact factor: 3.488

Review 4.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

5.  Recent Force Field Strategies for Intrinsically Disordered Proteins.

Authors:  Junxi Mu; Hao Liu; Jian Zhang; Ray Luo; Hai-Feng Chen
Journal:  J Chem Inf Model       Date:  2021-02-16       Impact factor: 4.956

6.  Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin.

Authors:  Bingbing Lin; Ya Gao; Yongxiu Li; John Z H Zhang; Ye Mei
Journal:  J Mol Model       Date:  2014-03-27       Impact factor: 1.810

7.  Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.

Authors:  Hao Wang; Weitao Yang
Journal:  J Chem Phys       Date:  2016-06-14       Impact factor: 3.488

8.  Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations.

Authors:  Haixin Wei; Ruxi Qi; Junmei Wang; Piotr Cieplak; Yong Duan; Ray Luo
Journal:  J Chem Phys       Date:  2020-09-21       Impact factor: 3.488

9.  A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation.

Authors:  Li Xiao; Qin Cai; Zhilin Li; Hongkai Zhao; Ray Luo
Journal:  Chem Phys Lett       Date:  2014-11-25       Impact factor: 2.328

10.  Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.

Authors:  Abhishek A Kognole; Asaminew H Aytenfisu; Alexander D MacKerell
Journal:  J Mol Model       Date:  2020-05-24       Impact factor: 1.810

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