Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase

详细信息    查看全文

• 作者：Andreas P. Eichenberger ; Wei Huang ; Sereina Riniker ; Wilfred F. van Gunsteren
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2015
• 出版时间：July 14, 2015
• 年：2015
• 卷：11
• 期：7
• 页码：2925-2937
• 全文大小：455K
• ISSN：1549-9626

文摘

A supra-atomic coarse-grained (CG) force field for liquid n-alkanes is presented. The model was calibrated using experimental thermodynamic data and structural as well as energetic properties for 14 n-alkanes as obtained from atomistic fine-grained (FG) simulations of the corresponding hydrocarbons using the GROMOS 45A3 biomolecular force field. A variation of the nonbonded force-field parameters obtained from mapping the FG interactions onto the CG degrees of freedom to fit the density and heat of vaporization to experimental values turned out to be mandatory for a correct reproduction of these data by the CG model, while the bonded force-field parameters for the CG model could be obtained from a Boltzmann-weighted fit with some variations with respect to the corresponding properties from the FG simulations mapped onto the CG degrees of freedom. The model presents 6 different CG bead types, for bead sizes from 2 to 4 distinguishing between terminal and nonterminal beads within an alkane chain (end or middle). It contains different nonbonded Lennard-Jones parameters for the interaction of CG alkanes with CG water. The CG alkane model was further tested by comparing predictions of the excess free energy, the self-diffusion constant, surface tension, isothermal compressibility, heat capacity, thermal expansion coefficient, and shear viscosity for n-alkanes to experimental values. The CG model offers a thermodynamically calibrated basis for the development of CG models of lipids.