聚合物内坐标分子动力学的拟Hamilton运动方程
Quasi-Hamiltonian Equations of Motion for Internal Coordinate Molecular Dynamics of Polymers
摘要：
传统的分子动力学模拟大分子需要很长的计算时间，因为与限制积分时间步长的键长和键角的快速振荡相比，最感兴趣的运动非常慢。在内部坐标空间中的动力学模拟，即键长，键角和扭转作为独立变量，给出了从系统中消除所有不感兴趣的快速自由度的理论可能性。提出了一种新的大分子内坐标分子动力学模拟方法。运动方程推导出适用于任何数量的内部自由度的支链分子。方程使用规范变量，它们比现有的类似物简单得多。在数值试验中，将内坐标动力学与传统的笛卡尔坐标分子动力学在56个残基的球状蛋白质的模拟中进行了比较。结果表明，传统的和内部的坐标动力学需要相同的时间步长相同的精度和氨基酸的标准几何近似，即与固定的键长，键角和刚性芳香族基团，特征步长为4秒，这是2倍高于固定的键长。当氢原子的旋转被抑制时，步长可以增加到11 fsec。
英文摘要：
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration time step. Simulation of dynamics in the space of internal coordinates, that is with bond lengths, bond angles and torsions as independent variables, gives a theoretical possibility to eliminate all uninteresting fast degrees of freedom from the system. This paper presents a new method for internal coordinate molecular dynamics simulations of macromolecules. Equations of motion are derived which are applicable to branched chain molecules with any number of internal degrees of freedom. Equations use the canonical variables and they are much simpler than existing analogs. In the numerical tests the internal coordinate dynamics are compared with the traditional Cartesian coordinate molecular dynamics in simulations a 56 residue globular protein. It is shown that the traditional and internal coordinate dynamics require the same time step size for the same accuracy and that in the standard geometry approximation of amino acids, that is with fixed bond lengths, bond angles and rigid aromatic groups, the characteristic step size is 4 fsec, that is two times higher than with fixed bond lengths only. The step size can be increased up to 11 fsec when rotation of hydrogen atoms is suppressed.
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