SUBSPACE METHOD FOR LONG-TIME SCALE MOLECULAR-DYNAMICS
SUBSPACE METHOD FOR LONG-TIME SCALE MOLECULAR-DYNAMICS
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DOI：
10.1021/j100019a017
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发表时间：
1995-05-11
影响因子：
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通讯作者：
RABITZ, H
中科院分区：
文献类型：
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作者：
ASKAR, A;SPACE, B;RABITZ, H
本文介绍了分子动力学方程长时间积分方法的双重基础。这项工作表明，长时间尺度的分子动力学发生在一个相对低维的子空间由一组集体本征模跨越，分子保持在这个子空间的时间跨度长，至少在皮秒或更大的顺序。这两点是中央构造一个有效的数值算法的长时间尺度动力学。第一点允许对动态的高频分量进行自动滤波，从而能够稳定地使用非常大的时间步长。第二个观察允许可能在长时间跨度内使用相同的基组。计算证实了这些点。模型分子由32个原子的链组成，其平衡构型是螺旋。链的相互作用是一个两个，三个和四体的性质，分别允许拉伸，弯曲和扭转运动。分子被有意地选择为经历极端的动态变化，以用于断言1和断言2以及所得到的算法的严格测试。此外，选择一个远离热平衡的初始状态，分子的所有能量驻留在平衡构型的单个局部正常模式中。另一个初始条件，与热分布的动能，进行了探讨。所提出的方法被证明是能够处理这两个不同的初始条件。动力学结果允许对问题的谱方面进行详细的分析，并为子空间概念和基于子空间的方法提供进一步的支持。对时间步长为delta t = 100 fs的稳定子空间动力学积分进行了计算，结果与全动力学结果吻合良好（使用标准分子动力学的最大允许时间步长将是Δ T近似于1fs）;动力学包括扭转势垒交叉。
This article presents the dual foundations of an approach to the long time integration of molecular dynamics equations. This work demonstrates that the long time scale molecular dynamics takes place in a relatively low dimensional subspace spanned by a set of collective eigenmodes and that the molecule remains in this subspace for long spans of time, at least on the order of picoseconds or greater. Both of these points are central to constructing an efficient numerical algorithm for long time scale dynamics. The first point allows for automatic filtering of the high frequency components of the dynamics and thus enables the stable use of very large time steps. The second observation allows for possibly using the same basis set for a long time span. Calculations are presented to substantiate these points. The model molecule consists of a 32 atom chain for which the equilibrium configuration is a helix. The chain interactions are of a two, three, and four body nature, allowing respectively for stretch, bending, and torsional motions. The molecule is intentionally chosen to undergo extreme dynamical changes for a severe test of both assertions 1 and 2 and the resulting algorithm. Moreover, one initial state is chosen very far from thermal equilibrium, with all of the energy of the molecule residing in a single local normal mode of the equilibrium configuration. Another initial condition, with a thermal distribution of kinetic energy, is explored. The methods presented are shown to be capable of handling both diverse initial conditions. The dynamical results permit a detailed analysis of the spectral aspects of the problem and provide further support for the subspace concept and the methodology based on it. Stable subspace dynamic integration for time steps of delta t = 100 fs were executed, and the results agree well with the full dynamics (for which the maximum allowable time step using standard molecular dynamics would be delta t approximate to 1 fs); the dynamics included torsional barrier crossings.