The ionic atmosphere around highly charged molecules, like DNA, involves a complex interplay of co-ions, counter-ions and water.  Rigorously modeling such an environment requires accounting for the discrete molecular nature of the solvent. The reference interaction site model (RISM) uses explicit molecular solvent models to provide a complete equilibrium sampling of bulk solvent and solvent around a solute of arbitrary shape and size.  Results are similar to those obtained from explicit solvent molecular dynamics (MD) but at a fraction of the cost. I will discuss three applications: to 'ion counting' experiments for DNA and RNA; to the calculation of SAXS and WAXS X-ray scattering profiles for proteins and nucleic acids; and to the study of disordered (or 'bulk') water in macromolecular crystals.

Simulating biomolecules with 3D-RISM implicit solvent models

248th National Meeting (2014)

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