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  • Simulation Best Practices for Lipid Membranes [Article v1. 0]
    In this section, we provide a checklist for the four major steps in the lipid membrane simulation process: (1) model selection, (2) pre-simulation considerations, including selection of MD settings, (3) preparation of initial configurations, and (4) post-simulation considerations, including validation of calculated properties
  • Membrane thickness, lipid phase and sterol type are . . . - Nature
    By combining stopped-flow kinetic measurements with molecular dynamics simulations, we performed a systematic analysis of the permeability of a variety of small molecules through synthetic
  • FATSLiM: a fast and robust software to analyze MD simulations . . .
    Without losing accuracy when performing analysis of flat membranes, this approach makes FATSLiM the first tool available to extract thickness, membrane area or APL from a MD simulations of distorted bilayers or vesicles
  • Dual Resolution Membrane Simulations Using Virtual Sites
    In Table S1, we report that membrane thickness and order parameter increase with the cutoff, while area per lipid and diffusion constant show an opposite trend This is because a longer cutoff has stronger nonbonded interactions, which can order the lipid arrangement
  • 7. 3: Molecular Dynamics for Biomembranes - Physics LibreTexts
    Incorporation of boundary conditions allows researchers to reduce the size of a simulation without sacrificing pertinent information One can run the desired simulation on the smallest possible unit, and surround it with replicas extending infinitely in all directions This results in a “bigger” simulation that still requires minimal computation
  • A review on models and simulations of membrane formation via . . .
    Firstly, one can easily understand that the membrane formation induced by energy variation and nonsolvent intrusion should involve three closely related transport phenomena: fluid dynamics, heat transfer, and mass transfer





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