QM/MM Tutorials for MTR1

QM/MM simulations of MTR1

• Generating umbrella windows for a 1-dimensional methyl transfer reaction in MTR1
  • Learning objectives
  • Relevant literature
  • Introduction
  • QM region selection
  • Preparing the inputs
  • Determine reaction coordinates
  • Generate the equilibration directory
  • Generate the umbrella windows
• Run 1-dimensional umbrella sampling
  • Learning objectives
  • Relevant literature
  • Running the umbrella sampling
• Analyze a 1-dimensional PMF from umbrella sampling
  • Learning objectives
  • Relevant literature
  • Generating the PMF
• Combining sampling from multiple trials
  • Learning objectives
  • Relevant literature
  • Generating a combined PMF
• Additional exercise: Demonstrating the impact of umbrella window spacing
  • Learning objectives
  • Relevant literature
  • Analyze different windows spacings
• Finding a minimum free energy path using the Surface Accelerated String Method (SASM)
  • Learning objectives
  • Relevant literature
  • Introduction
  • Running SASM simulations
• Analyzing a surface generated with the Surface Accelerated String Method (SASM)
  • Learning objectives
  • Relevant literature
  • Analyzing a set of strings
• Visualizing the path progression
  • Learning objectives
  • Relevant literature
  • Make a path progression movie
• Comparing the PMF at the semi-empirical and ab initio level
  • Learning objectives
  • Relevant literature
  • Comparing the PMF at the semi-empirical and ab initio level
  • References