生物分子绝对自由能的简单估算
Simple estimation of absolute free energies for biomolecules
摘要：
自由能差计算在分子系统中是众所周知的困难的一个原因是由于感兴趣的两个状态或系统之间的构象重叠或相似性不足。然而，如果可以计算出每个状态的绝对自由能，则重叠的程度是无关紧要的。我们提出了一种计算绝对自由能的方法，该方法采用了一个简单的结构，一个可精确计算的参考系，它与感兴趣的状态具有高度的重叠。该方法只需要通过模拟生成的构象的物理系综，以及近似相等的中央处理单元（CPU）成本的辅助计算。此外，即使在物理系综不完整或分布不当的情况下，计算也可以收敛到正确的自由能值。作为一个“证明的原则”，我们使用的方法来正确地预测自由能的测试系统的绝对值可以准确地计算，并预测亮氨酸二肽在隐式溶剂中的构象平衡。
英文摘要：
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is irrelevant, however, if the absolute free energy of each state can be computed. We present a method for calculating the absolute free energy that employs a simple construction of an exactly computable reference system which possesses high overlap with the state of interest. The approach requires only a physical ensemble of conformations generated via simulation, and an auxiliary calculation of approximately equal central-processing-unit (CPU) cost. Moreover, the calculations can converge to the correct free energy value even when the physical ensemble is incomplete or improperly distributed. As a "proof of principle," we use the approach to correctly predict free energies for test systems where the absolute values can be calculated exactly, and also to predict the conformational equilibrium for leucine dipeptide in implicit solvent.
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