Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program,Journal of Computational Chemistry

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Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2022-04-29 , DOI: 10.1002/jcc.26877
Marcus Wieder ₁ , Markus Fleck ₂ , Benedict Braunsfeld ₂ , Stefan Boresch ₂

Affiliation

We describe the theory of the so-called common-core/serial-atom-insertion (CC/SAI) approach to compute alchemical free energy differences and its practical implementation in a Python package called Transformato. CC/SAI is not tied to a specific biomolecular simulation program and does not rely on special purpose code for alchemical transformations. To calculate the alchemical free energy difference between several small molecules, the physical end-states are mutated into a suitable common core. Since this only requires turning off interactions, the setup of intermediate states is straightforward to automate. Transformato currently supports CHARMM and OpenMM as back ends to carry out the necessary molecular dynamics simulations, as well as post-processing calculations. We validate the method by computing a series of relative solvation free energy differences.

中文翻译：

没有速度限制的炼金术自由能模拟。独立于基础分子动力学程序计算自由能差异的通用框架

我们描述了计算炼金术自由能差的所谓共核/串行原子插入 (CC/SAI) 方法的理论及其在名为 Transformato 的 Python 包中的实际实现。CC/SAI 不依赖于特定的生物分子模拟程序，也不依赖于特殊用途的代码进行炼金术转换。为了计算几个小分子之间的炼金术自由能差，物理终态被突变为合适的共同核心。由于这只需要关闭交互，中间状态的设置很容易实现自动化。Transformato 目前支持 CHARMM 和 OpenMM 作为后端，以执行必要的分子动力学模拟以及后处理计算。

更新日期：2022-04-29

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