Enhanced configurational sampling in binding free-energy calculations

Article Abstract:

The newly developed method of replica -exchange thermodynamic integration (RETI) is studied and compared with finite-difference thermodynamic integration (FDTI) on the calculation of the relative binding free energies of halides to a calix [4] pyrrole derivative. The results show that the sampling of RETI is superior to that of FDTI at no additional computational costs.

United States, Evaluation, Measurement, Gibbs' free energy, Thermodynamic potentials

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A quantitative coarse-grain model for lipid bilayers

Article Abstract:

A simplified particle-based computer model is developed for hydrated phospholipid bilayers and is applied to quantitatively predict the major physical features of fluid-phase biomembranes. This coarse-grain model is directly compatible with atomic-level force fields, which has allowed mixed systems to be simulated in a multiscale fashion.

Usage, Computer simulation, Computer-generated environments, Hydrocarbons, Lipid membranes, Mechanical properties

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Prediction of partition coefficients by multistate hybrid atomic-level/coarse-grain simulations

Article Abstract:

Coarse-grain model is used for conducting mixed atomic-level and coarse-grain simulations of molecular systems. This coarse-grain force has retained electrostatic interactions, thus enabling the simplified solvent particles to interact realistically with the all-atom solutes.

Analysis, Solvents, Solution (Chemistry), Solutions (Chemistry), Electrostatic interactions, Atomic properties

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