LNB-MDT: Lipid NanoBubble Molecular Dynamics Toolbox

LNB-MDT (Lipid NanoBubble Molecular Dynamics Toolbox) is a comprehensive toolbox designed for molecular dynamics analysis of lipid nanobubbles.

Features

Graphical User Interface Modules

LNB-MDT provides three main functional modules:

Preparation Module

Analysis Module

Visualization Module

Molecular Dynamics Analysis

LNB-MDT provides various analysis types:

Area Per Lipid

Lipid-level; LNB-level

Anisotropy

LNB-level

Cluster Analysis

LNB-level

Order Parameter

Lipid-level; LNB-level

Gyration

LNB-level

Density

LNB-level

Graphical User Interface

  • Modern Qt6 interface design

  • Intuitive data visualization

  • Drag-and-drop file operations

  • VMD integration support

High-Performance Computing

  • Parallel processing support

  • Configurable computation parameters

  • Optimized algorithm implementation

Simplified Command Line Interface

  • Short Parameter Aliases: All parameters have short aliases (e.g., -g for --gro-file)

  • Simplified Input Formats: Support intuitive formats like DPPC:PO4,CHOL:ROH

  • Backward Compatibility: Traditional formats are still fully supported

Contents

Documentation

Indices and tables