Performing solvation free energy calculations in LAMMPS using the decoupling approach

Vikram Khanna; Jacob I Monroe; Michael F Doherty; Baron Peters

doi:10.1007/s10822-020-00303-3

Performing solvation free energy calculations in LAMMPS using the decoupling approach

J Comput Aided Mol Des. 2020 Jun;34(6):641-646. doi: 10.1007/s10822-020-00303-3. Epub 2020 Feb 28.

Authors

Vikram Khanna¹, Jacob I Monroe¹, Michael F Doherty¹, Baron Peters²

Affiliations

¹ Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
² Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, IL, 61801, USA. baronp@illinois.edu.

PMID: 32112288
DOI: 10.1007/s10822-020-00303-3

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.

Keywords: LAMMPS; Molecular dynamics; Solvation free energies; Thermodynamic integration.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Biphenyl Compounds / chemistry
Energy Metabolism*
Entropy
Ethanol / chemistry
Molecular Dynamics Simulation*
Software
Solutions / chemistry*
Thermodynamics*

Substances

Biphenyl Compounds
Solutions
diphenyl
Ethanol