Reproduction of macroscopic properties of unsaturated triacylglycerides using a modified NERD force field

Cordina, Robert J; Smith, Beccy; Tuttle, Tell

doi:10.1016/j.jmgm.2021.107996

Cited by 6 publications

(12 citation statements)

References 22 publications

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“…To calculate the LJ function between two different beads, the Lorentz–Berthelot mixing rules , were employed. The standard Coulomb potential was chosen as no reaction-field is used, as per our previous study . Non-bonded interactions between atoms which are one bond away were excluded.…”

Section: Resultsmentioning

confidence: 99%

“…All simulations were carried out using GROMACS 2019.3. The FF parameters for the UA simulations were the same as described previously . All UA equilibrations were carried out using an isobaric/isothermal (NPT) ensemble, using a v-rescale thermostat and a Berendsen barostat.…”

Section: Methodsmentioning

confidence: 99%

“…The standard Coulomb potential was chosen as no reaction-field is used, as per our previous study. 1 Non-bonded interactions between atoms which are one bond away were excluded. The COGITO FF potential is given in eq 1. , respectively.…”

Section: ■ Computational Methodsmentioning

confidence: 99%

“…In previous work, 1 we described the amendment of the NERD force field (FF) to reproduce the macroscopic properties of unsaturated triacylglycerides (TAGs) accurately. This is a united-atom (UA) FF, that is, one where methine, methylene, and methyl groups are all considered as one “heavy atom” rather than two, three, or four separate atoms, respectively.…”

Section: Introductionmentioning

confidence: 99%

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COGITO: A Coarse-Grained Force Field for the Simulation of Macroscopic Properties of Triacylglycerides

Cordina

Smith

Tuttle

2023

J. Chem. Theory Comput.

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The use of molecular dynamics simulations is becoming ever more widespread; however, the application of this to pure triacylglyceride (TAG) systems is not. In this study, we are presenting the development, and validation, of a new force field (FF), which we have called the COarse-Grained Interchangeable Triacylglyceride-Optimized FF. The FF has been developed using both a bottom-up and top-down approach for different parameters, with the non-bonded parameters being optimized using a Bayesian optimization method. While the FF was developed using monounsaturated TAGs, results show that it is also suitable for fully saturated TAGs. Description of molecules which were not used during the development of the FF is carried out simply by interchanging the bead in the molecule topologies. Results show that the FF can reproduce the macroscopic properties (density and lattice parameters) of pure TAGs as both crystals and melt with high accuracy, as well as reproduce the differences in enthalpies.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: ■ Computational Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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COGITO: A Coarse-Grained Force Field for the Simulation of Macroscopic Properties of Triacylglycerides

Cordina

Smith

Tuttle

2023

J. Chem. Theory Comput.

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“…The first simulation box contained 168 molecules (7 × 1 × 6 unit cells, with each unit cell having four molecules) in a single β 2 polymorph crystal and 32 molecules placed randomly around the crystal, giving, at the starting point, 84% of the molecules which are crystalline and 16% which are not ( Figure 1 ). The system was equilibrated using the modified NERD force field, 21 with the first 25 ns at 273 K, after which the temperature was raised to 373 K over 10 ps, and held at that temperature up to a total of 50 ns.…”

Section: Methodsmentioning

confidence: 99%

Rapid Automated Quantification of Triacylglyceride Crystallinity in Molecular Dynamics Simulations

Cordina

Smith

Tuttle

2022

J. Chem. Inf. Model.

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The relative stability of crystalline polymorphs and the transition between crystalline and melt phases are key parameters in determining the physical properties of triacylglycerides used in food. However, while the determination of properties experimentally is well-defined, the ability to predict the onset of melting and discriminate between polymorphs is less well-defined within a molecular dynamics simulation environment. In this work, we present metrics for measuring the crystallinity, including a new metric, the near-neighbor occupancy time, giving a rapid determination of how many, and which, molecules are found in a crystal over a simulation trajectory, and the polymorphic determination of triacylglycerides over a simulation trajectory.

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Polymorphic phase transitions in triglycerides and their mixtures studied by SAXS/WAXS techniques: In bulk and in emulsions

Cholakova,

Denkov

2024

Advances in Colloid and Interface Science

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Reproduction of macroscopic properties of unsaturated triacylglycerides using a modified NERD force field

Cited by 6 publications

References 22 publications

COGITO: A Coarse-Grained Force Field for the Simulation of Macroscopic Properties of Triacylglycerides

COGITO: A Coarse-Grained Force Field for the Simulation of Macroscopic Properties of Triacylglycerides

Rapid Automated Quantification of Triacylglyceride Crystallinity in Molecular Dynamics Simulations

Polymorphic phase transitions in triglycerides and their mixtures studied by SAXS/WAXS techniques: In bulk and in emulsions

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