Paper Citing NAMD - Abstract
Bhatnagar, Navendu; Kamath, Ganesh; Chelst, Issac; Potoff, Jeffrey J.
Direct calculation of 1-octanol-water partition coefficients from adaptive biasing force molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 014502, JUL 7 2012
The 1-octanol-water partition coefficient log K-ow of a solute is a key parameter used in the prediction of a wide variety of complex phenomena such as drug availability and bioaccumulation potential of trace contaminants. In this work, adaptive biasing force molecular dynamics simulations are used to determine absolute free energies of hydration, solvation, and 1-octanol-water partition coefficients for n-alkanes from methane to octane. Two approaches are evaluated; the direct transfer of the solute from 1-octanol to water phase, and separate transfers of the solute from the water or 1-octanol phase to vacuum, with both methods yielding statistically indistinguishable results. Calculations performed with the TIP4P and SPC/E water models and the TraPPE united-atom force field for n-alkanes show that the choice of water model has a negligible effect on predicted free energies of transfer and partition coefficients for n-alkanes. A comparison of calculations using wet and dry octanol phases shows that the predictions for log K-ow using wet octanol are 0.2-0.4 log units lower than for dry octanol, although this is within the statistical uncertainty of the calculation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4730040]
