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Items: 1 to 20 of 95

1.
2.

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

Lin Y, Baumketner A, Deng S, Xu Z, Jacobs D, Cai W.

J Chem Phys. 2009 Oct 21;131(15):154103. doi: 10.1063/1.3245232.

3.

Ionic solvation studied by image-charge reaction field method.

Lin Y, Baumketner A, Song W, Deng S, Jacobs D, Cai W.

J Chem Phys. 2011 Jan 28;134(4):044105. doi: 10.1063/1.3530094.

4.

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

Baker K, Baumketner A, Lin Y, Deng S, Jacobs D, Cai W.

Comput Phys Commun. 2013 Jan 1;184(1):19-26. Epub 2012 Aug 14.

5.

Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.

Song W, Lin Y, Baumketner A, Deng S, Cai W, Jacobs DJ.

Commun Comput Phys. 2013;13(2013):129-149.

6.

Three-dielectric-layer hybrid solvation model with spheroidal cavities in biomolecular simulations.

Xue C, Deng S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jan;81(1 Pt 2):016701. Epub 2010 Jan 5.

PMID:
20365496
7.

An n log n Generalized Born Approximation.

Anandakrishnan R, Daga M, Onufriev AV.

J Chem Theory Comput. 2011 Mar 8;7(3):544-59. doi: 10.1021/ct100390b. Epub 2011 Jan 27.

PMID:
26596289
8.

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.

Shivakumar D, Deng Y, Roux B.

J Chem Theory Comput. 2009 Apr 14;5(4):919-30. doi: 10.1021/ct800445x. Epub 2009 Mar 24.

PMID:
26609601
9.

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.

Xu Z, Cai W.

SIAM Rev Soc Ind Appl Math. 2011 Nov 7;53(4):683-720.

10.
11.

Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules.

Qin P, Xu Z, Cai W, Jacobs D.

Commun Comput Phys. 2009 Nov;6(5):955-977.

12.

Charge-dependent cavity radii for an accurate dielectric continuum model of solvation with emphasis on ions: aqueous solutes with oxo, hydroxo, amino, methyl, chloro, bromo, and fluoro functionalities.

Ginovska B, Camaioni DM, Dupuis M, Schwerdtfeger CA, Gil Q.

J Phys Chem A. 2008 Oct 23;112(42):10604-13. doi: 10.1021/jp804092v. Epub 2008 Sep 25.

PMID:
18816107
13.

SM6:  A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters.

Kelly CP, Cramer CJ, Truhlar DG.

J Chem Theory Comput. 2005 Nov;1(6):1133-52. doi: 10.1021/ct050164b.

PMID:
26631657
14.

Simulations of solvation and solvation dynamics in an idealized ionic liquid model.

Roy D, Maroncelli M.

J Phys Chem B. 2012 May 24;116(20):5951-70. doi: 10.1021/jp301359w. Epub 2012 May 11.

PMID:
22515910
15.
17.

Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges.

Marenich AV, Olson RM, Kelly CP, Cramer CJ, Truhlar DG.

J Chem Theory Comput. 2007 Nov;3(6):2011-33. doi: 10.1021/ct7001418.

PMID:
26636198
19.

Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics.

Wang J, Tan C, Chanco E, Luo R.

Phys Chem Chem Phys. 2010 Feb 7;12(5):1194-202. doi: 10.1039/b917775b. Epub 2009 Dec 23.

PMID:
20094685
20.

Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation.

Wang Z, Che J, Cheng LT, Dzubiella J, Li B, McCammon JA.

J Chem Theory Comput. 2012 Feb 14;8(2):386-397. Epub 2011 Dec 19.

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