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

Vikram Khanna, Jacob I. Monroe, Michael F. Doherty, Baron Peters

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Pages (from-to)	641-646
Number of pages	6
Journal	Journal of Computer-Aided Molecular Design
Volume	34
Issue number	6
DOIs	https://doi.org/10.1007/s10822-020-00303-3
State	Published - Jun 1 2020

Keywords

LAMMPS
Molecular dynamics
Solvation free energies
Thermodynamic integration

ASJC Scopus subject areas

Drug Discovery
Computer Science Applications
Physical and Theoretical Chemistry

Online availability

10.1007/s10822-020-00303-3

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title = "Performing solvation free energy calculations in LAMMPS using the decoupling approach",

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",

author = "Vikram Khanna and Monroe, {Jacob I.} and Doherty, {Michael F.} and Baron Peters",

note = "Funding Information: 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. Publisher Copyright: {\textcopyright} 2020, Springer Nature Switzerland AG.",

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doi = "10.1007/s10822-020-00303-3",

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AU - Khanna, Vikram

AU - Monroe, Jacob I.

AU - Doherty, Michael F.

AU - Peters, Baron

N1 - Funding Information: 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. Publisher Copyright: © 2020, Springer Nature Switzerland AG.

PY - 2020/6/1

Y1 - 2020/6/1

N2 - 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.

AB - 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.

KW - LAMMPS

KW - Molecular dynamics

KW - Solvation free energies

KW - Thermodynamic integration

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Performing solvation free energy calculations in LAMMPS using the decoupling approach

Abstract

Keywords

ASJC Scopus subject areas

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