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Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

Rosta E, Haranczyk M, Chu ZT, Warshel A.

J Phys Chem B. 2008 May 8;112(18):5680-92. doi: 10.1021/jp711496y. Epub 2008 Apr 16.

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Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules.

Schaefer P, Riccardi D, Cui Q.

J Chem Phys. 2005 Jul 1;123(1):014905.

PMID:
16035867
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Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.

Reif MM, Oostenbrink C.

J Comput Chem. 2014 Jan 30;35(3):227-43. doi: 10.1002/jcc.23490. Epub 2013 Nov 19.

11.

Fragment-based quantum mechanical methods for periodic systems with Ewald summation and mean image charge convention for long-range electrostatic interactions.

Zhang P, Truhlar DG, Gao J.

Phys Chem Chem Phys. 2012 Jun 7;14(21):7821-9. doi: 10.1039/c2cp23758j. Epub 2012 May 2.

12.

On removal of charge singularity in Poisson-Boltzmann equation.

Cai Q, Wang J, Zhao HK, Luo R.

J Chem Phys. 2009 Apr 14;130(14):145101. doi: 10.1063/1.3099708.

PMID:
19368474
13.

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

Wang J, Deng Y, Roux B.

Biophys J. 2006 Oct 15;91(8):2798-814. Epub 2006 Jul 14.

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Implementation of the solvent macromolecule boundary potential and application to model and realistic enzyme systems.

Zienau J, Cui Q.

J Phys Chem B. 2012 Oct 18;116(41):12522-34. doi: 10.1021/jp308218m. Epub 2012 Oct 5.

PMID:
22985044
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Strategy using three layers of surface charge for computing solvation free energy of ions.

Yang PK.

Biophys Chem. 2013 Dec 31;184:87-94. doi: 10.1016/j.bpc.2013.09.007. Epub 2013 Oct 8.

PMID:
24157373
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Continuum solvent studies of the stability of RNA hairpin loops and helices.

Srinivasan J, Miller J, Kollman PA, Case DA.

J Biomol Struct Dyn. 1998 Dec;16(3):671-82.

PMID:
10052623
20.

Restoring charge asymmetry in continuum electrostatics calculations of hydration free energies.

Purisima EO, Sulea T.

J Phys Chem B. 2009 Jun 18;113(24):8206-9. doi: 10.1021/jp9020799.

PMID:
19459599
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