在 LAMMPS 中使用解耦方法进行溶剂化自由能计算。
Performing solvation free energy calculations in LAMMPS using the decoupling approach.
机构信息
Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, IL, 61801, USA.
出版信息
J Comput Aided Mol Des. 2020 Jun;34(6):641-646. doi: 10.1007/s10822-020-00303-3. Epub 2020 Feb 28.
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.
去耦法计算溶剂化自由能要求在保留所有分子内相互作用的情况下，对溶剂和溶液之间的相互作用进行缩放。本文报告了一种新的方法，使这一计算在 LAMMPS 中成为可能。该程序通过内置的 GROMACS 功能进行了测试。选择乙醇和联苯作为测试我们方法的模型化合物。得到的 LAMMPS 和 GROMACS 结果相互吻合。这项工作将有助于在 LAMMPS 和/或其他没有内置功能实现去耦方法的分子动力学软件中进行溶剂化自由能计算。
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