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首页> 外文期刊>Journal of Computational Physics >A new FFF-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation
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A new FFF-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation

机译：一种基于FFF的新算法，用于在生物分子溶剂化的广义Born理论中计算Born半径

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In this paper, a new method for calculating effective atomic radii within the generalized Born (GB) model of implicit solvation is proposed, for use in computer simulations of biomolecules. First, a new formulation for the GB radii is developed, in which smooth kernels are used to eliminate the divergence in volume integrals intrinsic in the model. Next, the fast Fourier transform (FFT) algorithm is applied to integrate smoothed functions, taking advantage of the rapid spectral decay provided by the smoothing. The total cost of the proposed algorithm scales as O(N-3 log N + M) where M is the number of atoms comprised in a molecule and N is the number of FFT grid points in one dimension, which depends only on the geometry of the molecule and the spectral decay of the smooth kernel but not on M. To validate our algorithm, numerical tests are performed for three solute models: one spherical object for which exact solutions exist and two protein molecules of differing size. The tests show that our algorithm is able to reach the accuracy of other existing GB implementations, while offering much lower computational cost. (C) 2008 Elsevier Inc. All rights reserved.
机译：本文提出了一种在广义Born（GB）隐式溶剂化模型中计算有效原子半径的新方法，可用于生物分子的计算机模拟。首先，开发了GB半径的新公式，其中使用平滑核来消除模型固有的体积积分的差异。接下来，利用快速傅里叶变换（FFT）算法来整合平滑函数，从​​而利用平滑提供的快速频谱衰减。提出的算法的总成本为O（N-3 log N + M），其中M是分子中包含的原子数，N是一维FFT网格点的数量，仅取决于几何形状。为了验证我们的算法，对三个溶质模型进行了数值测试：一个存在精确解的球形物体和两个大小不同的蛋白质分子，以验证我们的算法。测试表明，我们的算法能够达到其他现有GB实现的精度，同时提供更低的计算成本。 （C）2008 Elsevier Inc.保留所有权利。

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