Journal of Chemical Theory and Computation · 2013 · 21 citations · 50 references
EngineeringLiquid-liquid FlowFluid MechanicsSoft Restraining PotentialsComputational ChemistryChemistryWater MoleculesSimple LiquidNumerical SimulationMulti-resolution ModelingMultiscale SimulationFour-to-one MappingBiophysicsPhysicsPhysical ChemistryMolecular MechanicMultiphase FlowLiquid WaterNatural SciencesCivil EngineeringHydrogen-bonded LiquidFluid-solid InteractionInterfacial StudyComputational BiophysicsMultiscale Modeling
We present a multiresolution simulation scheme for the solvent environment where four atomistic water molecules are mapped onto one coarse-grained bead. Soft restraining potentials are used to allow a resolution exchange of four water molecules into a single coarse-grained site. We first study the effect of adding restraining potentials in liquid water using full all-atom simulations. The usage of very soft restraining potentials to bundle four nearest neighbor water molecules does not disrupt the hydrogen bonding patterns in the liquid water. The structural properties of the first solvation shell around hydrophobic, hydrophilic, and ionic solutes are well preserved when soft restraining potentials are added. By modeling a bundle of four water molecules as a single molecule, a smooth transition and free exchange between coarse-grained and all-atom resolution is possible by using the adaptive resolution scheme (AdResS).
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GROMACS: Fast, flexible, and free
David van der Spoel, Erik Lindahl, Berk Hess et al. · Journal of Computational Chemistry · 2005 · 18.4K citations