High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations Article Swipe
Matthew Saunders
,
Vered Wineman‐Fisher
,
Eric Jakobsson
,
Sameer Varma
,
Sagar Pandit
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1021/acs.langmuir.1c03105
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1021/acs.langmuir.1c03105
Molecular dynamics (MD) force fields for lipids and ions are typically developed independently of one another. In simulations consisting of both lipids and ions, lipid-ion interaction energies are estimated using a predefined set of mixing rules for Lennard-Jones (LJ) interactions. This, however, does not guarantee their reliability. In fact, compared to the quantum mechanical reference data, Lorentz-Berthelot mixing rules substantially underestimate the binding energies of Na+ ions with small-molecule analogues of lipid headgroups, yielding errors on the order of 80 and 130 kJ/mol, respectively, for methyl acetate and diethyl phosphate. Previously, errors associated with mixing force fields have been reduced using approaches such as "NB-fix" in which LJ interactions are computed using explicit cross terms rather than those from mixing rules. Building on this idea, we derive explicit lipid-ion cross terms that also may implicitly include many-body cooperativity effects. Additionally, to account for the interdependency between cross terms, we optimize all cross terms simultaneously by performing high-dimensional searches using our ParOpt software. The cross terms we obtain reduce the errors due to mixing rules to below 10 kJ/mol. MD simulation of the lipid bilayer conducted using these optimized cross terms resolves the structural discrepancies between our previous simulations and small-angle X-ray and neutron scattering experiments. These results demonstrate that simulations of lipid bilayers with ions that are accurate up to structural data from scattering experiments can be performed without explicit polarization terms. However, it is worth noting that such NB-fix cross terms are not based on any physical principle; a polarizable lipid model would be more realistic and is still desired. Our approach is generic and can be applied to improve the accuracies of simulations employing mixed force fields.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acs.langmuir.1c03105
- OA Status
- green
- Cited By
- 13
- References
- 64
- Related Works
- 10
- OpenAlex ID
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https://openalex.org/W4213452100Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1021/acs.langmuir.1c03105Digital Object Identifier
- Title
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High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular SimulationsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
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2022-02-22Full publication date if available
- Authors
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Matthew Saunders, Vered Wineman‐Fisher, Eric Jakobsson, Sameer Varma, Sagar PanditList of authors in order
- Landing page
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https://doi.org/10.1021/acs.langmuir.1c03105Publisher landing page
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
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https://www.ncbi.nlm.nih.gov/pmc/articles/9801415Direct OA link when available
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Chemistry, Force field (fiction), Ion, Mixing (physics), Molecular dynamics, Combining rules, Molecule, Cooperativity, Statistical physics, Molecular physics, Computational chemistry, Physics, Quantum mechanics, Mathematics, Biochemistry, Arithmetic, Binary number, Organic chemistryTop concepts (fields/topics) attached by OpenAlex
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13Total citation count in OpenAlex
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2025: 5, 2024: 2, 2023: 5, 2022: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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