Nikitin Alexei M, Milchevskiy Yury V, Lyubartsev Alexander P
Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, 119991, Russia,
J Mol Model. 2014 Mar;20(3):2143. doi: 10.1007/s00894-014-2143-6. Epub 2014 Feb 19.
We present a new force field parameter set for simulating alkanes. Its functional form and parameters are chosen to make it directly compatible with the AMBER94/99/12 family of force fields implemented in the available software. The proposed parameterization enables universal description of both the conformational and thermodynamic properties of linear, branched, and cyclic alkanes. Such unification is achieved by using two essential principles: (1) reduction of the Lennard-Jones radius for all sp3 carbons to 1.75Å; (2) separate optimization of Lennard-Jones well depths for carbons with different degree of substitution. The new parameter set may prove to be optimal for description of alkyl residues in a broad range of biomolecules, from amino acids to lipids with their extended linear tails.
我们提出了一种用于模拟烷烃的新力场参数集。其函数形式和参数的选择使其能直接与现有软件中实现的AMBER94/99/12系列力场兼容。所提出的参数化方法能够对线性、支链和环状烷烃的构象和热力学性质进行通用描述。这种统一是通过两个基本原理实现的：（1）将所有sp3碳的 Lennard-Jones 半径减小到1.75Å；（2）对不同取代度的碳分别优化 Lennard-Jones 阱深。新参数集可能被证明是描述从氨基酸到具有延伸线性尾部的脂质等广泛生物分子中烷基残基的最佳选择。
