Chapter 19: Free Energy Landscapes

Question 1

Free Energy Landscapes

Answer 1

• GOAL: map energy landscape between different conformations
  
  • achieved by looking at free energy differences
    
    • unrealistic to sample all of phase space

Question 2

Free Energy Landscapes (Intermediate States)

Answer 2

• usually states X, Y are close, but if not, can use set of intermediate states I_i
  
  • _​I_i need not be physica
  • X, Y must be physical

Question 3

Thermodynamic Integration

Answer 3

try to find reversible path between states X, Y

• assume potential (see below)

Question 4

Metadynamics

Answer 4

• define bias potentials
• take “negative” to get potential
• tricky part is defining collective variable s
  
  • anything geometry related, path, coordination number, etc.