Free energy perturbation study of octanol/water partition coefficients: comparison with continuum GB/SA calculations

Article Abstract:

Molecular dynamics (MD) free energy perturbation (FEP) calculations are used to gain insight into the thermodynamics and structure of a series of small organic molecules in a box of water-saturated octanol. Both aqueous and water-saturated octanol free energies of solvation were determined in order to calculate relative partition coefficients for each perturbation. The results of the FEP calculations were in good agreement with experimental relative partition coefficients, deltalog rho(sub ow), except for the acetamide-acetone perturbation.

Analysis, Solvents, Perturbation (Quantum dynamics), Perturbation (Mathematics)

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Application of a multiple time step algorithm to biomolecular systems

Article Abstract:

Three biomolecular systems were used to test the effectiveness of the multiple time step (MTS) method against the traditional SHAKE method. These systems are an antifreeze peptide in water, the organic solvent dimethylformamide and a dimyristoylphosphatidylcholine-based lipid bilayer. Results showed that the MTS method, in contrast to the SHAKE method, can produce stable trajectories even when a long time step is used and does not disturb the bond vibrational motion.

Methods, Lipid membranes, Bilayer lipid membranes, Vibrational spectra, Dimethylformamide

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