#39 · Structural bio & protein design
Unsupervised lipid packing analysis resolves coexisting phases in MD bilayer simulations
Across these items, the common thread is methodology for extracting structural and phase information from molecular dynamics trajectories of lipid membranes and confined liquids. A preprint examines how POPC bilayer size (256 to 1024 lipids) and hydration affect lipid membrane analysis, benchmarking CPPTRAJ, GROMACS, MDAnalysis, and LiPyphilic. A published study introduces an unsupervised approach that pixelates lipid packing density and applies a two-component threshold to classify coexisting lipid phases in bilayer simulations. DynoPore, a published Python package, addresses structure, mobility, and lifetimes for liquids confined in pores. The new element is the unsupervised phase-recognition route, set alongside systematic assessment of system size and software dependence.
Published papers
DynoPore─A Package to Analyze Molecular Dynamics Trajectories of Confined Liquids.
DynoPore is a Python package for analyzing molecular dynamics trajectories of liquids confined in pores, covering structure, mobility, lifetimes, and ionic…
Recognition of Coexisting Phases in Model Membranes via an Unsupervised Method.
Unsupervised method classifies coexisting lipid phases in MD bilayer simulations by pixelating lipid packing density and thresholding with a two-component…
Preprints
Bigger Isn't Always Better: Comparing System Size, Hydration, and Software for Lipid Membrane Analysis
MD of POPC bilayers (256-1024 lipids) tests size and hydration effects; benchmarks CPPTRAJ, GROMACS, MDAnalysis, LiPyphilic.
Topic history
| Date | Rank |
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| #39 |