A Poisson-Boltzmann dynamics method with nonperiodic boundary condition
A Poisson-Boltzmann dynamics method with nonperiodic boundary condition
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DOI：
10.1063/1.1622376
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发表时间：
2003-12-01
影响因子：
4.4
通讯作者：
Luo, R
中科院分区：
文献类型：
--
作者：
Lu, Q;Luo, R
我们开发了一种具有非周期边界条件的良好且高效的有限差分泊松-玻尔兹曼动力学方法。这在一定程度上是通过用于反应场相互作用的有限差分处理的相当细的网格间距来实现的。这种稳定性还可以通过新的介电模型实现，该模型在时间和空间上都很平滑，这是隐式溶剂应用中的一个重要问题。此外，静电聚焦技术有利于使用准确而有效的非周期性边界条件：通过各个网格电荷的电势总和计算出边界网格电势。最后，在库仑相互作用的计算中采用粒子-粒子粒子-网格技术来平衡大生物分子模拟的精度和效率。初步测试表明，非周期泊松-玻尔兹曼动力学方法在至少 4 ns 长的轨迹上是数值稳定的。新模型也相当高效：它与成对广义 Born 溶剂模型相当，使其成为稀水溶液中生物分子动力学模拟的有力候选者。请注意，当前对总静电相互作用的处理是没有截止的，这对于生物分子的模拟很重要。在泊松-玻尔兹曼框架内也可以对德拜-休克尔筛选进行严格处理：其重要性通过高电荷蛋白质的模拟得到证明。 (C) 2003 年美国物理研究所。
We have developed a well-behaved and efficient finite difference Poisson-Boltzmann dynamics method with a nonperiodic boundary condition. This is made possible, in part, by a rather fine grid spacing used for the finite difference treatment of the reaction field interaction. The stability is also made possible by a new dielectric model that is smooth both over time and over space, an important issue in the application of implicit solvents. In addition, the electrostatic focusing technique facilitates the use of an accurate yet efficient nonperiodic boundary condition: boundary grid potentials computed by the sum of potentials from individual grid charges. Finally, the particle-particle particle-mesh technique is adopted in the computation of the Coulombic interaction to balance accuracy and efficiency in simulations of large biomolecules. Preliminary testing shows that the nonperiodic Poisson-Boltzmann dynamics method is numerically stable in trajectories at least 4 ns long. The new model is also fairly efficient: it is comparable to that of the pairwise generalized Born solvent model, making it a strong candidate for dynamics simulations of biomolecules in dilute aqueous solutions. Note that the current treatment of total electrostatic interactions is with no cutoff, which is important for simulations of biomolecules. Rigorous treatment of the Debye-Huckel screening is also possible within the Poisson-Boltzmann framework: its importance is demonstrated by a simulation of a highly charged protein. (C) 2003 American Institute of Physics.