Internal coordinate molecular dynamics: a foundation for multiscale dynamics.
Internal coordinate molecular dynamics: a foundation for multiscale dynamics.
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DOI：
10.1021/jp509136y
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发表时间：
2015-01-29
期刊：
影响因子：
--
通讯作者：
Jain A
中科院分区：
文献类型：
--
作者：
Vaidehi N;Jain A
键长、键角和扭转角(BAT)等内部坐标是描述键合分子体系的自然坐标。然而，由于运动方程的数学简单性，广泛用于蛋白质、DNA和聚合物的分子动力学(MD)模拟方法是基于笛卡尔坐标的。然而，笛卡尔分子动力学模拟常常需要约束来增强构象采样。这使得笛卡尔坐标下的运动方程是微分代数的，这对仿真的复杂性和稳健性产生了不利的影响。另一方面，通过删除需要约束的自由度，可以在BAT坐标中轻松放置约束。因此，内部坐标MD(ICMD)为发展多尺度MD方法提供了一个有吸引力的替代笛卡尔坐标MD的方法。扭转MD方法是ICMD方法的一种特殊适应，所有的键长和键角都是刚性的。ICMD模拟方法的优点是冻结高频自由度并在更重要的低频扭转自由度中进行构象搜索，从而提供更长的时间步长。然而，ICMD模拟的进展缓慢，并被长期存在的数学瓶颈所扼杀。在这篇综述中，我们总结了基于空间算子代数在开发适用于各种应用的健壮的长时间尺度ICMD仿真工具方面所取得的最新数学进展。我们还介绍了ICMD模拟在研究蛋白质构象变化和蛋白质结构优化方面的应用。我们回顾了ICMD模拟相对于笛卡尔模拟的优势，并展望了ICMD模拟在蛋白质动力学中的未来应用。
Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics.
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