通过结合预先计算的分子片段库估计绝对自由能
Absolute free energies estimated by combining pre-calculated molecular fragment libraries
摘要：
分子的绝对自由能--或者等价地说是配分函数--可以用合适的参考系通过计算来估计。在这里，我们展示了一个实用的方法，通过一系列片段的基础上生长的分子进行这样的计算。通过预先计算片段构型和相互作用，节省了大量的计算机时间，以便在各种分子中重复使用。我们采用这样的片段库和氨基酸和封端基团的相互作用表来估计小肽的自由能。分子的平衡系综产生在没有额外的计算成本，并用于检查我们的结果相比，标准的动力学模拟。
英文摘要：
The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule based on a series of fragments. Significant computer time is saved by pre-calculating fragment configurations and interactions for re-use in a variety of molecules. We employ such fragment libraries and interaction tables for amino acids and capping groups to estimate free energies for small peptides. Equilibrium ensembles for the molecules are generated at no additional computational cost, and are used to check our results by comparison to standard dynamics simulation.
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