Tsui V, Case D A
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Biopolymers. 2000;56(4):275-91. doi: 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E.
Generalized Born (GB) models provide an attractive way to include some thermodynamic aspects of aqueous solvation into simulations that do not explicitly model the solvent molecules. Here we discuss our recent experience with this model, presenting in detail the way it is implemented and parallelized in the AMBER molecular modeling code. We compare results using the GB model (or GB plus a surface-area based "hydrophobic" term) to explicit solvent simulations for a 10 base-pair DNA oligomer, and for the 108-residue protein thioredoxin. A slight modification of our earlier suggested parameters makes the GB results more like those found in explicit solvent, primarily by slightly increasing the strength of NH [bond] O and NH [bond] N internal hydrogen bonds. Timing and energy stability results are reported, with an eye toward using these model for simulations of larger macromolecular systems and longer time scales.
广义玻恩（GB）模型提供了一种颇具吸引力的方法，可将水合作用的一些热力学方面纳入到未明确对溶剂分子进行建模的模拟中。在此，我们讨论我们近期使用该模型的经验，详细介绍其在AMBER分子建模代码中的实现和并行化方式。我们将使用GB模型（或GB加上基于表面积的“疏水”项）得到的结果与针对一个10碱基对的DNA寡聚物以及108个残基的蛋白质硫氧还蛋白进行的显式溶剂模拟结果进行比较。对我们之前建议的参数进行轻微修改后，GB结果更类似于显式溶剂中的结果，主要是通过略微增强N-H⋯O和N-H⋯N分子内氢键的强度实现的。本文报告了计时和能量稳定性结果，旨在将这些模型用于更大的大分子系统和更长时间尺度的模拟。
