Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations

Leonard, Alison N.; Simmonett, Andrew C.; Pickard, Frank C.; Huang, Jing; Venable, Richard M.; Klauda, Jeffery B.; Brooks, Bernard R.; Pastor, Richard W.

doi:10.1021/acs.jctc.7b00948

Cited by 59 publications

(101 citation statements)

References 73 publications

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“…Calculated viscosities at three temperatures for hexadecane simulated with C36 and Drude (symbols) with a cutoff Lennard-Jones (top) and with LJ-PME (bottom). 105 Experimental values for hexadecane (C16), pentadecane (C15) and tetradecane (C14) in lines. Log-log plots of the inverse of the oxygen diffusion constant in alkanes vs. alkane viscosity from simulation and experiment; linear fits in dotted lines.…”

Section: Discussionmentioning

confidence: 99%

Molecular Dynamics Simulations of Membrane Permeability

2019

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This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of non-biological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Lastly, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.

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Section: Discussionmentioning

confidence: 99%

Molecular Dynamics Simulations of Membrane Permeability

2019

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“…61,62 This method prevents what would otherwise be a discontinuity in the forces at the cutoff distance, but does introduce complexity when switching from direct to reciprocal space combining rules. 15 The overlap damped dispersion PME model avoids this by explicitly parameterizing to a multiplicative combining rule. This implementation is certainly not unique or novel, but it is important to the future use of the overlap damped dispersion model in a complete force field because it shows that the benefit of a more physics-based short-range model can be realized at no increase in cost.…”

Section: Dispersion Particle Mesh Ewald Summationmentioning

confidence: 99%

“…13,14 Additionally, longrange dispersion is widely recognized to be important for the simulation of lipid bilayers. 15 This broad spectrum of applications motivates the necessity of accurate dispersion models.…”

Section: Introductionmentioning

confidence: 99%

A physically grounded damped dispersion model with particle mesh Ewald summation

Rackers

Liu

Ren

et al. 2018

The Journal of Chemical Physics

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Accurate modeling of dispersion is critical to the goal of predictive biomolecular simulations. To achieve this accuracy, a model must be able to correctly capture both the short-range and asymptotic behavior of dispersion interactions. We present here a damped dispersion model based on the overlap of charge densities that correctly captures both regimes. The overlap damped dispersion model represents a classical physical interpretation of dispersion: the interaction between the instantaneous induced dipoles of two distinct charge distributions. This model is shown to be an excellent fit with symmetry adapted perturbation theory dispersion energy calculations, yielding an RMS error on the S101x7 database of 0.5 kcal/mol. Moreover, the damping function used in this model is wholly derived and parameterized from the electrostatic dipole-dipole interaction, making it not only physically grounded but transferable as well.

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“…Therefore, researchers must conform to the standard Lennard-Jones (LJ) cutoff scheme recommended for the force field. In the future, lipid parameterization will include the use of PME for LJ interactions [94] to avoid this artificial cutoff dependence.…”

Section: Survey Of Lipid Membrane Modelsmentioning

confidence: 99%

Simulation Best Practices for Lipid Membranes [Article v1.0]

Smith¹,

Klauda²,

Sodt³

2019

LiveCoMS

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We establish a reliable and robust standardization of settings for practical molecular dynamics (MD) simulations of pure and mixed (single-and multi-component) lipid bilayer membranes. In lipid membranes research, particle-based molecular simulations are a powerful tool alongside continuum theory, lipidomics, and model, in vitro, and in vivo experiments. Molecular simulations can provide precise and reproducible spatiotemporal (atomic-and femtosecond-level) information about membrane structure, mechanics, thermodynamics, kinetics, and dynamics. Yet the simulation of lipid membranes can be a daunting task, given the uniqueness of lipid membranes relative to conventional liquid-liquid and solid-liquid interfaces, the immense and complex thermodynamic and statistical mechanical theory, the diversity of multiscale lipid models, limitations of modern computing power, the difficulty and ambiguity of simulation controls, finite size effects, competitive continuum simulation alternatives, and the desired application, including vesicle experiments and biological membranes. These issues can complicate an essential understanding of the field of lipid membranes, and create major bottlenecks to simulation advancement. In this article, we clarify these issues and present a consistent, thorough, and user-friendly framework for the design of state-of-the-art lipid membrane MD simulations. We hope to allow early-career researchers to quickly overcome common obstacles in the field of lipid membranes and reach maximal impact in their simulations.

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Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations

Cited by 59 publications

References 73 publications

Molecular Dynamics Simulations of Membrane Permeability

Molecular Dynamics Simulations of Membrane Permeability

A physically grounded damped dispersion model with particle mesh Ewald summation

Simulation Best Practices for Lipid Membranes [Article v1.0]

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