Explicit solvent atomistic molecular dynamics (MD) simulations represent an established technique to study structural dynamics of RNA molecules and an important complement for diverse experimental methods. However, performance of molecular mechanical (MM) force fields (ffs) remains far from satisfactory even after decades of development, as apparent from a problematic structural description of some important RNA motifs. Actually, some of the smallest RNA molecules belong to the most challenging systems for MD simulations and, among them, the UNCG tetraloop is saliently difficult. We report a detailed analysis of UNCG MD simulations, depicting the sequence of events leading to the loss of the UNCG native state during MD simulations. We identify molecular interactions, backbone conformations and substates that are involved in the process. The total amount of MD simulation data analyzed in this work is close to 1.3 millisecond. Then, we unravel specific ff deficiencies using diverse quantum mechanical/molecular mechanical (QM/MM) and QM calculations. Comparison between the MM and QM methods shows discrepancies in the description of the 5`-flanking phosphate moiety and both signature sugar-base interactions. Our work indicates that poor behavior of the UNCG tetraloop in simulations is a complex issue that cannot be attributed to one dominant and straightforwardly correctable factor. Instead, there is a concerted effect of multiple ff inaccuracies that are coupled and amplifying each other. We attempted to improve the simulation behavior by some carefully-tailored interventions but the results are still far from satisfactory, underlying the difficulties in development of accurate nucleic acids ffs.

中文翻译：

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UNCG RNA四环是MD模拟中的强大力场挑战

显式溶剂原子分子动力学（MD）模拟代表了一种研究RNA分子结构动力学的成熟技术，并且是多种实验方法的重要补充。但是，即使经过几十年的发展，分子机械力（MM）力场（ffs）的性能仍然远远不能令人满意，这从对一些重要RNA图案的结构性描述上有问题。实际上，某些最小的RNA分子属于MD模拟中最具挑战性的系统，而其中UNCG四环非常困难。我们报告了对UNCG MD模拟的详细分析，描绘了导致MD模拟过程中UNCG原始状态丧失的事件序列。我们确定过程中涉及的分子相互作用，骨架构象和亚状态。这项工作中分析的MD仿真数据总量接近1.3毫秒。然后，我们使用各种量子力学/分子力学（QM / MM）和QM计算方法来解决特定的ff缺陷。MM方法和QM方法之间的比较显示，在5'侧翼磷酸部分的描述以及两个标志性糖基相互作用中均存在差异。我们的工作表明，模拟中UNCG四环的不良行为是一个复杂的问题，不能归因于一个主要且直接可纠正的因素。取而代之的是多个ff误差相互关联并相互放大的协同效应。我们尝试通过一些精心设计的干预措施来改善模拟行为，但结果仍远远不能令人满意，