Department of Chemistry, Hanyang University, Seoul 133-792, Korea.
J Phys Chem A. 2012 Nov 29;116(47):11763-7. doi: 10.1021/jp309150r. Epub 2012 Nov 13.
Presented are parameters for mono-, di-, and trivalent cations compatible with the CHARMM additive force field and the TIP3P water model. Thermodynamic perturbation molecular dynamics simulations were performed for the cations located at the center of a TIP3P water sphere under a solvent boundary potential. A series of perturbations generated free energies of hydration indexed by the two Lennard-Jones parameters, ε and R(min). Interpolating the experimental free energies of hydration showed that multiple combinations of ε and R(min) values reproduced the free energies of hydration for each ion. To overcome this nonunique parameter problem, the hydration shell model in combination with an empirical scaling parameter was applied to assign values for each ion. R(min) values were then identified via interpolation of the calculated free energies of hydration. The presented parameters are anticipated to be of utility for simulations of ions, including ions complexed to proteins.
本文介绍了与 CHARMM 加和力场和 TIP3P 水模型兼容的单价、二价和三价阳离子的参数。在溶剂边界势下，对位于 TIP3P 水球中心的阳离子进行了热力学微扰分子动力学模拟。通过一系列微扰生成了由两个 Lennard-Jones 参数 ε 和 R(min) 索引的水合自由能。内插实验水合自由能表明， ε 和 R(min) 值的多种组合可以重现每种离子的水合自由能。为了解决这个非唯一性参数问题，应用了水化壳模型结合经验缩放参数来为每个离子分配值。然后通过内插计算的水合自由能来确定 R(min) 值。预计本文介绍的参数对于离子模拟，包括与蛋白质结合的离子，将非常有用。
