Generalized solvent boundary potential

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... 

Im, W. Bernhche, S. Roux, B., Generalized solvent boundary potential for computer simulations, J. Chem. Phys. 2001,114, 2924-2937. 

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... 

QM and MM region, //mm represents the potential energy of the MM region, and i/b is an appropriate boundary potential taking into account the effect from the bulk solvent. The Hamiltonian //qm is identical to that used in QM calculations for an isolated molecule in the gas phase (see Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field), whereas //mm takes the same form of empirical potential energy expressions as those used in MM force fields (see Force Fields A General Discussion). 

If an electrolyte AB is distributed between two solvents, a and f3, there will in general be a difference of potential established across the boundary, due to the existence of a double layer ( 198). 

Electrophoresis. Electrophoresis, or cataphoresis as it is sometimes called, is concerned with the movement of colloidal particles in an electric field. A simple apparatus, due to Burton, by which the phenomenon of electrophoresis may be demonstrated, is shown in Fig. 3. The solvent is first poured into the tube, T, followed by the colloidal suspension. If precautions are taken to avoid mixing of the solutions, boundaries between the colloidal suspension and solvent will be present at equal heights, such as a-a, and these will be visible if the suspension is colored or turbid. If now a potential is applied at the electrodes E-Er the boundaries will, in general, move. Rough estimates of the mobilities of the colloidal particles may be obtained by measuring the distances passed through by the boundaries. However, there is little or... 

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