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Performing solvation free energy calculations in LAMMPS using the decoupling approach

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Abstract

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.

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Acknowledgements

We are grateful for the financial support provided by Eli Lilly. Use was made of computational facilities purchased with funds from the National Science Foundation (CNS-1725797) and administered by the Center for Scientific Computing (CSC). The CSC is supported by the California NanoSystems Institute and the Materials Research Science and Engineering Center (MRSEC; NSF DMR 1720256) at UC Santa Barbara.

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Authors and Affiliations

  1. Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA

    Vikram Khanna, Jacob I. Monroe & Michael F. Doherty

  2. Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, IL, 61801, USA

    Baron Peters

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  1. Vikram Khanna
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  2. Jacob I. Monroe
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  3. Michael F. Doherty
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  4. Baron Peters
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Correspondence to Baron Peters.

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Khanna, V., Monroe, J.I., Doherty, M.F. et al. Performing solvation free energy calculations in LAMMPS using the decoupling approach. J Comput Aided Mol Des 34, 641–646 (2020). https://doi.org/10.1007/s10822-020-00303-3

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  • DOI: https://doi.org/10.1007/s10822-020-00303-3

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