Question

What are the methods for calculating the free energy difference between two states? What are the roles of MD/MC simulations for calculating the free energy?

Name one of the enhanced sampling methods that utilize the Metropolis algorithm.

Answer 1

1.The methods for calculating the free energy difference between two states

Free Energy Perturbation
Thermodynamic Integration
Slow Growth Method
Umbrella Sampling and Histogram Methods
Weighted Histogram Analysis Method (WHAM)

2. the roles of MD/MC simulations for calculating the free energy?

when designing complex and hybrid molecular dynamic (MD) algorithms which  play a fundamental role in MC

In MD molecular dynamics shows the role played in proton conductance by the BM2 channel and for the influenza virus B-drug resistance

3. Enhanced sampling methods that utilize the Metropolis algorithm.

The collective-variables-based methods which includes the   variationally enhanced sampling and metadynamics. Then, collective variable free methods such as integrated tempering methods and parallel tempering
Selective integrated tempering sampling

Recents are
Partitioned ITS
Multiscale sampling: MetaITS
Optimization of collective variables
Sampling methods with deep learning: TALOS and others