Accelerated Poisson-Boltzmann calculations for static and dynamic systems
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
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DOI：
10.1002/jcc.10120
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发表时间：
2002-10-01
影响因子：
3
通讯作者：
Gilson, MK
中科院分区：
文献类型：
--
作者：
Luo, R;David, L;Gilson, MK
我们在此报告基于改进的不完全乔尔斯基共轭梯度算法的有限差分泊松-玻尔兹曼溶剂模型的有效实现，该算法为静态和动态系统提供了令人印象深刻的性能，这是通过使用 Eisenstat 的两种优化实现算法、在模拟中利用静电更新以及应用谨慎的近似来实现的，包括： 收敛准则，不每一步更新泊松-玻尔兹曼相关力，并使用静电聚焦，还可以显着加速用于建立计算和获取能量和力的支持例程。由此产生的有限差分泊松-玻尔兹曼方法的效率可与测试系统 HIV 蛋白酶的距离相关介电模型相媲美，使其成为溶液相分子动力学模拟的有力候选者。此外，有限差分法包括所有溶质内静电相互作用，而距离相关介电计算使用 15-A 截止值。我们的数值有限差分方法的速度与泊松-玻尔兹曼方法的成对广义玻恩近似的速度相当。
We report here an efficient implementation of the finite difference Poisson-Boltzmann solvent model based on the Modified Incomplete Cholsky Conjugate Gradient algorithm, which gives rattler impressive performance for both static and dynamic systems, This is achieved by implementing the algorithm with Eisenstat's two optimizations, utilizing the electrostatic update in simulations, and applying prudent approximations, including: relaxing the convergence criterion, not updating Poisson-Boltzmann-related forces every step, and using electrostatic focusing, It is also possible to markedly accelerate the supporting routines that are used to set up the calculations and to obtain energies and forces. The resulting finite difference Poisson-Boltzmann method delivers efficiency comparable to the distance-dependent dielectric model for a system tested, HIV Protease, making it a strong candidate for solution-phase Molecular dynamics simulations. Further, the finite difference method includes all intrasolute electrostatic interactions, whereas the distance dependent dielectric calculations use a 15-A cutoff. The speed of our numerical finite difference method is comparable to that of the pair-wise Generalized Born approximation to the Poisson-Boltzmann method.