Welcome to FATSLiM's documentation!

Release:0.2.1 Date:September 29, 2016

FATSLiM (Fast Analysis Toolbox for Simulations of Lipid Membranes - fatslim.github.io) is a software dedicated to the analysis of molecular dynamics simulations of lipid membranes.

It can read Gromacs file formats.

Contents:

• 1. Overview
• 2. Installing FATSLiM
  • 2.1. Requirements
  • 2.2. Pre-installation
  • 2.3. Installation
  • 2.4. Post-installation
• 3. User interface
  • 3.1. Command line interface
  • 3.2. General commands and options
  • 3.3. Analytical commands and related options
• 4. Leaflet and membrane identification
  • 4.1. How FATSLiM identifies leaflets and membranes
  • 4.2. Associated command and parameters
• 5. Thickness calculation
  • 5.1. How FATSLiM estimates membrane thickness
  • 5.2. Associated command and parameters
• 6. Membrane area and Area per lipid calculation
  • 6.1. How FATSLiM estimates membrane area and area per lipid
  • 6.2. Associated command and parameters
• 7. Tutorials & Examples
  • 7.1. Introduction
  • 7.2. Tutorial #1: Simple membrane identification
  • 7.3. Tutorial #2: Membrane thickness over trajectory
  • 7.4. Tutorial #3: Vesicle membrane area and area per lipid
  • 7.5. Tutorial #4: Extracting raw APL data for further processing

Indices and tables

• Index
• Module Index
• Search Page