Linear Scaling Electrostatic and Generalized Solvent Boundary Methods

Linear Scaling Electrostatic and Generalized Solvent Boundary Methods 

Giese and York (GY) [68] used the branch-free FMM algorithm of Watson et al. [69] and the recursive bisection ideas of Perez-Jorda and Yang (PJY) [70] to create an adaptive FMM for systems of particles composed of point multipoles, as opposed to the trivial case of point charges (monopoles). GY spent most of their effort in 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74], 

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 

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This section describes the main methodological advances that will be used in subsequent selected applications, including (1) Development of fast semiempirical methods for multiscale quantum simulations, (2) Directions for development of next-generation QM/MM models, and (3) Linear-scaling electrostatic and generalized solvent boundary methods. 

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