Course Details
Subject {L-T-P / C} : PH6124 : Classical Molecular Simulations { 3-0-0 / 3}
Subject Nature : Theory
Coordinator : Prof. Mithun Biswas
Syllabus
- Classical dynamics: Phase spaces and the Lagrangian and Hamiltonian formulations, the Liouville equation and equilibrium solutions, classical time evolution operator and numerical integrators, force field, molecular dynamics
- Thermodynamics of real gases and liquids: radial distribution function, Mayer f-function
- Dynamics on free energy surface: Non-equilibrium free energy methods, Jarzynski's and Crook's theorems, equilibrium free energy methods, free energy perturbation, thermodynamic integration
- Monte Carlo simulation: Importance sampling, Markov models, parallel tempering
- Stochastic dynamics: Derivation of generalized Langevin dynamics for model systems, fluctuation-dissipation theorem, memoryless Langevin and Brownian dynamics, probability distributions and Fokker-Planck equations
Course Objectives
- Understanding the basics of molecular simulations.
- Viewing molecular events as dynamics on the free energy landscape.
- Recovering kinetics of molecular reactions.
Course Outcomes
To gain expertise in application of statistical mechanics to molecular systems
Essential Reading
- H.J.C. Berendsen, Simulating the Physical World, Cambridge University Press
- M.P. Allen, D.J. Tildesley, Computer Simulation of Liquids, Oxford University Press
Supplementary Reading
- Mark E. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, Oxford University Press
- D. Frenkel, B. Smit, Understanding Molecular Simulations: From Algorithms to Applications, Academic Press