We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence.

中文翻译：

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分子动力学模拟中热平衡的新方法

我们描述了一种在分子动力学 (MD) 模拟过程中实现蛋白质和周围溶剂之间热平衡的简单新程序。该方法独特地定义了在广泛的参数范围内实现热平衡所需的模拟时间长度，从而消除了与传统启发式方法相关的歧义。所提出的协议节省了模拟时间并避免了由于包含非平衡事件而引入的偏差。该过程的关键要素涉及仅将溶剂原子耦合到标准热浴。测量热平衡的进展涉及简单地监测溶剂和蛋白质之间的温度差异。这里，