Solvent boundary potential

D. Beglov and B. Roux. Finite representation of an infinite bulk system Solvent boundary potential for computer simulations. J. Chem. Phys., 100 9050-9063, 1994. 

In finite boundary conditions the solute molecule is surrounded by a finite layer of explicit solvent. The missing bulk solvent is modeled by some form of boundary potential at the vacuum/solvent interface. A host of such potentials have been proposed, from the simple spherical half-harmonic potential, which models a hydrophobic container [22], to stochastic boundary conditions [23], which surround the finite system with shells of particles obeying simplified dynamics, and finally to the Beglov and Roux spherical solvent boundary potential [24], which approximates the exact potential of mean force due to the bulk solvent by a superposition of physically motivated tenns. 

B. Solvent Boundary Potentials and Implicit/Explicit Mixed Schemes... 

Variational electrostatic projection method. In some instances, the calculation of PMF profiles in multiple dimensions for complex chemical reactions might not be feasible using full periodic simulation with explicit waters and ions even with the linear-scaling QM/MM-Ewald method [67], To remedy this, we have developed a variational electrostatic projection (VEP) method [75] to use as a generalized solvent boundary potential in QM/MM simulations with stochastic boundaries. The method is similar in spirit to that of Roux and co-workers [76-78], which has been recently... 

Banavali, N.K. Im, W. Roux, B., Electrostatic free energy calculations using the generalized solvent boundary potential method, J. Chem. Phys. 2002,117,7381-7388. 

Beglov, D. and Roux, B. (1994) Finite Representation of an Infinite Bulk System Solvent Boundary Potential for Computer Simulations, J. Chem. Phys. 100, 9050-9063. 

Benighaus, T., Thiel, W. Efficiency and accuracy of the generalized solvent boundary potential for hybrid QM/MM simulations Implementation for semiempirical Hamiltonians. J. Chem. Theor. Comp. 2008,4,1600-9. 

The energetics of proton transfer along the water chains can be evaluated using methods that combine QM for a system, MM (or MD) for the protein (including internal water), and continuum electrostatics for external solvent and the membrane. (The latter can treated via generalized solvent boundary potential (GSBP) [139]). The methods of such calculations are currently well developed [32,140, 141-151], and have been reviewed recently [152], At the time of this writing, such... 

Boulanger, E., and W. Thiel, Solvent boundary potentials for hybrid QM/MM computations using classical Crude oscillators A fully polarizable model./ Chem. Theory Comput, 2012. 8(11], 4527-4538. 

Infinite Bulk System Solvent Boundary Potential for Computer Simulations. 

Beglov D, Roux B (1994) Finite representatirai of an infinite bulk system - solvent boundary potential for compuler-simulatirais. J Chem Phys 100 9050-9063... 

Im W, Bemeche S, Roux B (2001) Generalized solvent boundary potential for computer simulations. J Chem Phys 114 2924—2937... 

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