Chemical and Materials Physics Graduate Program, University of California, Irvine, California, 92697.
Department of Physics and Astronomy, University of California, Irvine, California, 92697.
J Comput Chem. 2017 May 30;38(14):1057-1070. doi: 10.1002/jcc.24782. Epub 2017 Mar 20.
Continuum solvent models, particularly those based on the Poisson-Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one-sided and two-sided methods with both first-order and second-order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces. These efforts prompted us to develop an efficient approximated one-dimensional method, which is to fit the surface field one dimension at a time, for biomolecular applications without much compromise in accuracy. We also developed a surface-to-atom force partition scheme given a level set representation of analytical molecular surfaces to facilitate their applications to molecular simulations. Testing of these fitting methods in the dielectric boundary force calculations shows that the second-order methods, including the one-dimensional method, consistently perform among the best in the molecular test cases. Finally, the timing analysis shows the approximated one-dimensional method is far more efficient than standard second-order methods in the PBE force calculations. © 2017 Wiley Periodicals, Inc.
连续溶剂模型，特别是基于泊松-玻尔兹曼方程（PBE）的模型，在生物分子结构和功能的研究中被广泛应用。现有的 PBE 发展主要集中在如何获得更准确和/或更有效的数值势和能量。然而，要将 PBE 模型应用于分子动力学模拟，一个困难是如何准确有效地解释介电边界力，以实现稳健的动力学模拟。本研究记录了一系列标准拟合方案的实现和分析，包括单边和双边方法，以及一阶和二阶泰勒展开，以计算分子表面电场，从而方便介电边界力的数值计算。这些努力促使我们开发了一种有效的近似一维方法，该方法可以在不牺牲精度的情况下，对生物分子应用进行一次一维拟合，以进行表面场拟合。我们还开发了一种表面到原子力分配方案，给定分析分子表面的水平集表示，以方便它们在分子模拟中的应用。这些拟合方法在介电边界力计算中的测试表明，二阶方法，包括一维方法，在分子测试案例中表现始终最好。最后，时间分析表明，在 PBE 力计算中，近似的一维方法比标准的二阶方法效率高得多。© 2017 威利父子公司。
