标题： 聚合物内坐标分子动力学的准哈密顿运动方程 显示英文标题

标题： Quasi-Hamiltonian Equations of Motion for Internal Coordinate Molecular Dynamics of Polymers

摘要： 常规分子动力学模拟大分子需要很长的计算时间，因为最有趣的运动相比键长和键角的快速振荡非常缓慢，这限制了积分时间步长。 在内部坐标空间中模拟动力学，即以键长、键角和二面角作为独立变量，理论上可以消除系统中所有不感兴趣的快速自由度。 本文提出了一种用于大分子内部坐标分子动力学模拟的新方法。 推导出了适用于任何数量内部自由度的分支链分子的运动方程。 这些方程使用规范变量，比现有的类似方法简单得多。 在数值测试中，内部坐标动力学与传统的笛卡尔坐标分子动力学在模拟一个56残基球状蛋白质时进行了比较。 结果表明，传统动力学和内部坐标动力学在相同精度下需要相同的时间步长，并且在氨基酸的标准几何近似下，即固定键长、键角和刚性芳香环时，特征步长为4飞秒，比仅固定键长时高出两倍。 当抑制氢原子旋转时，步长可以增加到11飞秒。 显示英文摘要

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.