Quick Start Guide

This guide will help you get started with LNB-MDT for lipid nanobubble analysis in 5 minutes.

Configure VMD Path

First-time use of LNB-MDT requires configuring the VMD path. VMD is used for molecular visualization and trajectory analysis.

Configure VMD Path Using Command Line (Recommended)

Use the built-in VMD configuration command:

LNB-MDT VMD --path /path/to/vmd

# Example for macOS
LNB-MDT VMD --path /Applications/VMD.app/Contents/MacOS/VMD

# Example for Linux
LNB-MDT VMD --path /usr/local/bin/vmd

# Example for Windows
LNB-MDT VMD --path "C:/Program Files/VMD/vmd.exe"

Or Edit Configuration File Manually

Open the config.ini file in the project root directory and modify vmd_path to your actual VMD installation path:

# Common path examples
Windows: C:/Program Files/VMD/vmd.exe
macOS:   /Applications/VMD.app/Contents/vmd/vmd_MACOSXARM64
Linux:   /usr/local/bin/vmd

Verify Configuration

Check if VMD path is correctly configured:

LNB-MDT VMD

Starting the Program

Graphical Interface Launch

Using the graphical interface is the easiest way to start using LNB-MDT:

# Launch GUI (after installation)
LNB-MDT UI

# Or simply (UI is the default)
LNB-MDT

After launching, you will see the LNB-MDT main interface with four functional modules: Generation, Analysis, Figure, and VMD modules. For detailed information about these modules, see the main Features section on the homepage.

Command Line Launch

For batch processing and automated analysis, you can use command-line tools:

# View help information
LNB-MDT --help

# View help for specific analysis
LNB-MDT AREA --help

Basic Analysis Workflow

Prepare Data Files

LNB-MDT requires the following files for analysis:

GRO/TPR file: Molecular coordinate structure file
XTC/TRR file: Molecular dynamics trajectory file

The project includes example data files: - cases/lnb.gro - Example GRO file - cases/md.xtc - Example XTC file

Select Analysis Type

LNB-MDT provides comprehensive analysis capabilities for lipid nanobubbles. For detailed information about each analysis type, see the main Features section on the homepage.

Running Analysis

Graphical Interface Execution

Load GRO and XTC files in the interface
Select analysis type
Configure parameters
Click the “Run” button
View results

Command Line Execution

LNB-MDT supports simplified command-line parameter input, making it easier to use command-line tools:

Short Parameter Alias Reference Table

Simplified residues and gas-group formats

# Simple format (recommended)
-r DPPC:PO4,CHOL:ROH
-a N2:N2

# Multi-atom format
-r DPPC:PO4+GLY,CHOL:ROH

# Traditional dictionary format (still supported)
-r "{'DPPC': ['PO4'], 'CHOL': ['ROH']}"

Using LNB-MDT command (recommended):

# Gyration analysis example with full parameters
LNB-MDT GYRATION \
  --gro-file cases/lnb.gro \
  --xtc-file cases/md.xtc \
  --output-csv results/gyration_results.csv \
  --residues "{'DPPC': ['PO4']}" \
  --parallel \
  --verbose

Simplified approach with short parameters:

# Using short parameters and simple format
LNB-MDT GYRATION \
  -g cases/lnb.gro \
  -x cases/md.xtc \
  -o results/gyration_results.csv \
  -r DPPC:PO4 \
  -p \
  -v

# Or use test mode for quick testing
LNB-MDT GYRATION -test

Viewing Results

After analysis completion, LNB-MDT generates the following outputs:

CSV files: Numerical data containing analysis results
Charts: Visualization of analysis results
Logs: Detailed information about the analysis process

Result interpretation:

View numerical results in CSV files
Use chart module to visualize data
Combine with VMD for molecular visualization

First-time use requires configuring the VMD path:

Find VMD Installation Path

Windows: Usually at C:/Program Files/VMD/vmd.exe
macOS:   Usually at /Applications/VMD.app/Contents/vmd/vmd_MACOSXARM64
Linux:   Usually at /usr/local/bin/vmd

Edit Configuration File

Open the config.ini file in the project root directory and modify vmd_path to your actual VMD installation path:

[VMD]
vmd_path = /Applications/VMD.app/Contents/vmd/vmd_MACOSXARM64

Verify Configuration

Save the configuration file and restart the LNB-MDT program.

Starting VMD

Graphical interface launch:

Click the “Start VMD” button
Wait for VMD to start
Drag CSV files to the VMD window
Select molecules for visualization

Next Steps

Congratulations! You have successfully completed the LNB-MDT quick start!

What you can do next:

Learn advanced usage of Analysis Modules Details
Check api_reference for API details