Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations.

Autor: Leonard AN; Biophysics Program, University of Maryland , College Park, Maryland 20742, United States., Simmonett AC; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States., Pickard FC 4th; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States., Huang J; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.; Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States., Venable RM; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States., Klauda JB; Biophysics Program, University of Maryland , College Park, Maryland 20742, United States.; Department of Chemical and Biomolecular Engineering, University of Maryland , College Park, Maryland 20742, United States., Brooks BR; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States., Pastor RW; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.
Jazyk: angličtina
Zdroj: Journal of chemical theory and computation [J Chem Theory Comput] 2018 Feb 13; Vol. 14 (2), pp. 948-958. Date of Electronic Publication: 2018 Jan 09.
DOI: 10.1021/acs.jctc.7b00948
Abstrakt: Long-range Lennard-Jones (LJ) interactions have a significant impact on the structural and thermodynamic properties of nonpolar systems. While several methods have been introduced for the treatment of long-range LJ interactions in molecular dynamics (MD) simulations, increased accuracy and extended applicability is required for anisotropic systems such as lipid bilayers. The recently refined Lennard-Jones particle-mesh Ewald (LJ-PME) method extends the particle-mesh Ewald (PME) method to long-range LJ interactions and is suitable for use with anisotropic systems. Implementation of LJ-PME with the CHARMM36 (C36) additive and CHARMM Drude polarizable force fields improves agreement with experiment for density, isothermal compressibility, surface tension, viscosity, translational diffusion, and 13 C T 1 relaxation times of pure alkanes. Trends in the temperature dependence of the density and isothermal compressibility of hexadecane are also improved. While the C36 additive force field with LJ-PME remains a useful model for liquid alkanes, the Drude polarizable force field with LJ-PME is more accurate for nearly all quantities considered. LJ-PME is also preferable to the isotropic long-range correction for hexadecane because the molecular order extends to nearly 20 Å, well beyond the usual 10-12 Å cutoffs used in most simulations.
Databáze: MEDLINE
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