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Performing solvation free energy calculations in LAMMPS using the decoupling approach.
Journal of Computer-Aided Molecular Design ( IF 3.0 ) Pub Date : 2020-02-28 , DOI: 10.1007/s10822-020-00303-3
Vikram Khanna 1 , Jacob I Monroe 1 , Michael F Doherty 1 , Baron Peters 2
Affiliation  

The decoupling approach to solvation free energy calculations requires scaling the interactions between the solute and the solution with all intramolecular interactions preserved. This paper reports a new procedure that makes it possible to these calculations in LAMMPS. The procedure is tested against built-in GROMACS capabilities. The model compounds chosen to test our methodology are ethanol and biphenyl. The LAMMPS and GROMACS results obtained are in good agreement with each other. This work should help perform solvation free energy calculations in LAMMPS and/or other molecular dynamics software having no built-in functions to implement the decoupling approach.

中文翻译:

使用解耦方法在 LAMMPS 中执行溶剂化自由能计算。

溶剂化自由能计算的解耦方法需要在保留所有分子内相互作用的情况下缩放溶质和溶液之间的相互作用。本文报告了一种新程序,可以在 LAMMPS 中进行这些计算。该过程针对内置 GROMACS 功能进行了测试。选择用于测试我们的方法的模型化合物是乙醇和联苯。获得的 LAMMPS 和 GROMACS 结果相互吻合。这项工作应该有助于在 LAMMPS 和/或其他没有内置函数来实现解耦方法的分子动力学软件中执行溶剂化自由能计算。
更新日期:2020-02-28
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