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Items: 1 to 20 of 345

1.

Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization.

Wang J, Cieplak P, Li J, Cai Q, Hsieh MJ, Luo R, Duan Y.

J Phys Chem B. 2012 Jun 21;116(24):7088-101. doi: 10.1021/jp3019759.

2.

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

Wang J, Cieplak P, Li J, Wang J, Cai Q, Hsieh M, Lei H, Luo R, Duan Y.

J Phys Chem B. 2011 Mar 31;115(12):3100-11. doi: 10.1021/jp1121382.

3.

Efficient optimization of van der Waals parameters from bulk properties.

Burger SK, Cisneros GA.

J Comput Chem. 2013 Oct 15;34(27):2313-9. doi: 10.1002/jcc.23376.

PMID:
23828265
4.
6.

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

Ren P, Wu C, Ponder JW.

J Chem Theory Comput. 2011 Oct 11;7(10):3143-3161.

7.

Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.

Calero CS, Farwer J, Gardiner EJ, Hunter CA, Mackey M, Scuderi S, Thompson S, Vinter JG.

Phys Chem Chem Phys. 2013 Nov 7;15(41):18262-73. doi: 10.1039/c3cp53158a.

PMID:
24064723
8.

Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.

Wu JC, Piquemal JP, Chaudret R, Reinhardt P, Ren P.

J Chem Theory Comput. 2010 Jul 13;6(7):2059-2070.

9.

Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field.

Chapman DE, Steck JK, Nerenberg PS.

J Chem Theory Comput. 2014 Jan 14;10(1):273-81. doi: 10.1021/ct400610x.

PMID:
26579910
10.

Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models.

Davis JE, Rahaman O, Patel S.

Biophys J. 2009 Jan;96(2):385-402. doi: 10.1016/j.bpj.2008.09.048.

11.

Continuum polarizable force field within the Poisson-Boltzmann framework.

Tan YH, Tan C, Wang J, Luo R.

J Phys Chem B. 2008 Jun 26;112(25):7675-88. doi: 10.1021/jp7110988.

14.

Relative complexation energies for Li(+) ion in solution: molecular level solvation versus polarizable continuum model study.

Eilmes A, Kubisiak P.

J Phys Chem A. 2010 Jan 21;114(2):973-9. doi: 10.1021/jp907359a.

PMID:
20030307
15.

Ab initio van der waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like.

Møgelhøj A, Kelkkanen AK, Wikfeldt KT, Schiøtz J, Mortensen JJ, Pettersson LG, Lundqvist BI, Jacobsen KW, Nilsson A, Nørskov JK.

J Phys Chem B. 2011 Dec 8;115(48):14149-60. doi: 10.1021/jp2040345.

PMID:
21806000
16.

Effects of truncating van der Waals interactions in lipid bilayer simulations.

Huang K, García AE.

J Chem Phys. 2014 Sep 14;141(10):105101. doi: 10.1063/1.4893965.

17.

Importance of van der Waals Interactions in QM/MM Simulations.

Riccardi D, Li G, Cui Q.

J Phys Chem B. 2004 May 20;108(20):6467-78. doi: 10.1021/jp037992q.

PMID:
18950136
18.

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate.

Zhang C, Lu C, Wang Q, Ponder JW, Ren P.

J Chem Theory Comput. 2015 Nov 10;11(11):5326-39. doi: 10.1021/acs.jctc.5b00562.

19.

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

Wang J, Cieplak P, Li J, Hou T, Luo R, Duan Y.

J Phys Chem B. 2011 Mar 31;115(12):3091-9. doi: 10.1021/jp112133g.

20.

Quantum mechanical continuum solvation models for ionic liquids.

Bernales VS, Marenich AV, Contreras R, Cramer CJ, Truhlar DG.

J Phys Chem B. 2012 Aug 2;116(30):9122-9. doi: 10.1021/jp304365v.

PMID:
22734466
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