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Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set
[Image: see text] The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resoluti...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9648188/ https://www.ncbi.nlm.nih.gov/pubmed/36190354 http://dx.doi.org/10.1021/acs.jctc.2c00524 |
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author | Oliveira, Marina P. Gonçalves, Yan M. H. Ol Gheta, S. Kashef Rieder, Salomé R. Horta, Bruno A. C. Hünenberger, Philippe H. |
author_facet | Oliveira, Marina P. Gonçalves, Yan M. H. Ol Gheta, S. Kashef Rieder, Salomé R. Horta, Bruno A. C. Hünenberger, Philippe H. |
author_sort | Oliveira, Marina P. |
collection | PubMed |
description | [Image: see text] The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρ(liq) and vaporization enthalpies ΔH(vap) of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard–Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κ(T), the isobaric thermal-expansion coefficient α(P), the isobaric heat capacity c(P), the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔG(wat), and the free energy of solvation ΔG(che) in cyclohexane. For the target properties ρ(liq) and ΔH(vap), the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κ(T), α(P), ϵ, D, and ΔG(che); and less accurate results in terms of c(P) and ΔG(wat). This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution. |
format | Online Article Text |
id | pubmed-9648188 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-96481882022-11-15 Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set Oliveira, Marina P. Gonçalves, Yan M. H. Ol Gheta, S. Kashef Rieder, Salomé R. Horta, Bruno A. C. Hünenberger, Philippe H. J Chem Theory Comput [Image: see text] The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρ(liq) and vaporization enthalpies ΔH(vap) of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard–Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κ(T), the isobaric thermal-expansion coefficient α(P), the isobaric heat capacity c(P), the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔG(wat), and the free energy of solvation ΔG(che) in cyclohexane. For the target properties ρ(liq) and ΔH(vap), the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κ(T), α(P), ϵ, D, and ΔG(che); and less accurate results in terms of c(P) and ΔG(wat). This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution. American Chemical Society 2022-10-03 2022-11-08 /pmc/articles/PMC9648188/ /pubmed/36190354 http://dx.doi.org/10.1021/acs.jctc.2c00524 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Oliveira, Marina P. Gonçalves, Yan M. H. Ol Gheta, S. Kashef Rieder, Salomé R. Horta, Bruno A. C. Hünenberger, Philippe H. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set |
title | Comparison of the
United- and All-Atom Representations
of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized
against the Same Experimental Data Set |
title_full | Comparison of the
United- and All-Atom Representations
of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized
against the Same Experimental Data Set |
title_fullStr | Comparison of the
United- and All-Atom Representations
of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized
against the Same Experimental Data Set |
title_full_unstemmed | Comparison of the
United- and All-Atom Representations
of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized
against the Same Experimental Data Set |
title_short | Comparison of the
United- and All-Atom Representations
of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized
against the Same Experimental Data Set |
title_sort | comparison of the
united- and all-atom representations
of (halo)alkanes based on two condensed-phase force fields optimized
against the same experimental data set |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9648188/ https://www.ncbi.nlm.nih.gov/pubmed/36190354 http://dx.doi.org/10.1021/acs.jctc.2c00524 |
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