MDToolbox

Introduction

• Introduction
  • What is MDToolbox?
  • Requirements
  • Download
  • Installation for MATLAB
  • Installation for Octave
  • Compiling MEX-files and multithreading
  • Docker image for MDToolbox
  • Summary of main functions
• Getting Started
  • Input/Output
  • Coordinate and trajectory variables
  • Atom selection

Examples

• 1D Umbrella Sampling of Tri-Alanine and WHAM
• 1D Umbrella Sampling of Tri-Alanine and dTRAM
• 1D Umbrella Sampling of Tri-Alanine and MBAR
• Conventional MD of Alanine-Dipeptide and 2D PMF surface
• 2D Umbrella Sampling of Alanine-Dipeptide and WHAM
• 2D Umbrella Sampling of Alanine-Dipeptide and MBAR
• Anisotropic Network Model
  • Normal mode analysis of ANM
  • Transformation of frame