Multiscale molecular dynamics using the matched interface and boundary method.
Multiscale molecular dynamics using the matched interface and boundary method.
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DOI：
10.1016/j.jcp.2010.09.031
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发表时间：
2011-01-20
影响因子：
4.1
通讯作者：
Wei, G. W.
中科院分区：
文献类型：
--
作者：
Geng, Weihua;Wei, G. W.
关键词：
泊松-玻尔兹曼（PB）方程是一种用于生物分子和其他介电系统静电分析的多尺度模型。基于PB的分子动力学（MD）方法具有处理大型生物系统的潜力。目前阻碍基于PB的MD方法发展的主要障碍是准确性、稳定性、效率和可靠性。复杂的溶剂-溶质界面、几何奇点和电荷奇点的存在给PB方程的数值求解和基于PB的MD方法中的静电力评估带来了挑战。近年来，利用匹配界面和边界（MIB）方法开发了一阶二阶精确PB求解器，该求解器在处理介电系数不连续、复杂几何奇点和奇异源电荷时具有数值稳定性。本工作利用MIB方法开发了基于PB的MD方法。新公式的静电力被导出，以允许使用尖锐的分子表面。通过对静电势直接求导，可以得到精确的反作用力。介质边界力在溶剂-溶质界面用精确的笛卡尔网格曲面积分法进行了计算。位于可重入表面的静电力被适当地分配给相关的原子。为了验证目前静电力计算的准确性和稳定性，进行了大量的数值试验。新的基于PB的MD方法与AMBER包一起实现。通过几个实例系统演示了基于MIB的生物分子动力学模拟。
The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.
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影响因子：
3
作者：
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通讯作者：
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