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An anisotropic coarse‐grained model based on G ay– B erne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model
Author(s) -
Shen Hujun,
Li Yan,
Xu Peijun,
Li Xiaofang,
Chu Huiying,
Zhang Dinglin,
Li Guohui
Publication year - 2015
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23895
Subject(s) - multipole expansion , van der waals force , dipole , molecular dynamics , chemistry , anisotropy , bilayer , lipid bilayer , chemical physics , work (physics) , molecule , solvent , computational chemistry , thermodynamics , physics , optics , biochemistry , organic chemistry , quantum mechanics , membrane
In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay–Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay–Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness ( D H H), area per lipid ( A L ) and volume per lipid ( V L ). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters were reproduced reasonably well by the GBEMP model, demonstrating the promising feature of GBEMP model in modeling lipid systems. Finally, we have shown that current GBEMP model is more efficient by a factor of about 25 than AMBER atomistic point charge model. © 2015 Wiley Periodicals, Inc.