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A multi-scale framework was recently proposed for more realistic moleculardynamics simulations in continuum solvent models by coupling a molecularmechanics treatment of solute with a fluid mechanics treatment of solvent,where we formulated the physical model and developed a numerical fluid dynamicsintegrator. In this study, we incorporated the fluid dynamics integrator withthe Amber simulation engine to conduct atomistic simulations of biomolecules.At this stage of the development, only nonelectrostatic interactions, i.e., vandel Waals and hydrophobic interactions are included in the multi-scale model.Nevertheless numerical challenges exist in accurately interpolating the highlynonlinear van del Waals term when solving the finite-difference fluid dynamicsequations. We were able to bypass the challenge rigorously by merging the vandel Waals potential and pressure together when solving the fluid dynamicsequations and by considering its contribution in the free-boundary conditionanalytically. The multi-scale simulation engine was first validated byreproducing the solute-solvent interface of a single atom with analyticalsolution. Next, we performed the relaxation simulation of a restrainedsymmetrical monomer and observed a symmetrical solvent interface at equilibriumwith detailed surface features resembling those found on the solvent excludedsurface. Four typical small molecular complexes were then tested, both volumeand force balancing analysis showing that these simple complexes can reachequilibrium within the simulation time window. Finally, we studied the qualityof the multi-scale solute-solvent interfaces for the four tested dimercomplexes and found they agree well with the boundaries as sampled in theexplicit water simulations.

journal of chemical physics online/the journal of chemical physics/journal of chemical physics

Exploring A Multi-Scale Method for Molecular Simulations in Continuum  Solvent Model: Explicit Simulation of Continuum Solvent As An Incompressible  Fluid