Performing solvation free energy calculations in LAMMPS using the decoupling approach

Autor:	Vikram Khanna, Jacob I. Monroe, Michael F. Doherty, Baron Peters
Rok vydání:	2020
Předmět:	Work (thermodynamics) Materials science Ethanol Entropy Biphenyl Compounds Solvation Thermodynamic integration Decoupling (cosmology) Molecular Dynamics Simulation Computer Science Applications Solutions Molecular dynamics Intramolecular force Drug Discovery Thermodynamics Statistical physics Physical and Theoretical Chemistry Energy Metabolism Scaling Software Energy (signal processing)
Zdroj:	Journal of Computer-Aided Molecular Design. 34:641-646
ISSN:	1573-4951 0920-654X
DOI:	10.1007/s10822-020-00303-3
Popis:	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.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8d269a85daac5e57c4b367004433b7d4 https://doi.org/10.1007/s10822-020-00303-3 Zobrazit plný text záznamu Plný text ve formátu PDF Plný text ve formátu HTML
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