The European Physical Journal E · 2009 · 266 citations · 44 references
Inverse Boltzmann MethodEngineeringHydrogeophysicsWater ClustersParticle MethodComputational ChemistryWater-rock InteractionSimple LiquidMolecular DynamicsEarth ScienceSedimentationMineral-fluid InteractionMolecular SimulationMolecular KineticsBiophysicsCoarse-grained StudyPhysicsPhysical ChemistryWet ChemistryMolecular MechanicSediment TransportWater ResourcesCoarse-grained PotentialsNatural SciencesApplied PhysicsComputational BiophysicsMultiscale Modeling
We employ the inverse Boltzmann method to coarse-grain three commonly used three-site water models (TIP3P, SPC and SPC/E) where one molecule is replaced with one coarse-grained particle with isotropic two-body interactions only. The shape of the coarse-grained potentials is dominated by the ratio of two lengths, which can be rationalized by the geometric constraints of the water clusters. It is shown that for simple two-body potentials either the radial distribution function or the geometrical packing can be optimized. In a similar way, as needed for multiscale methods, either the pressure or the compressibility can be fitted to the all atom liquid. In total, a speed-up by a factor of about 50 in computational time can be reached by this coarse-graining procedure.
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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