## Course Description

This course is on methods for molecular simulations.

**Instructor:** Dr. Nisanth N. Nair (Email: nnair@iitk.ac.in, Phone: 6311, Office, Southern Labs, 302)

**Lecture Hours:** W (09:00-10:15) F (09:00-10:15) **Lecture Room:** **Room No. 101A, New Core Labs (****Instrumentation Lab)**** **

**Office Hours:** Friday (12:00-13:30) Venue: Southern Labs 302

**Evaluations:**

3 Project works + 2 Written Exams (Midsem & Endsem)

**Exam Weights:** Projects: 3 x 20 %, Exams: 2 x 20%

**Grading:** A* > 90% , A > 75 %, B : 55 %, C: 35% , D: 15 %, F: otherwise

## Course Content

**Course Contents**

**1. Empirical Force-Fields, Molecular Dynamics and Monte Carlo Simulations.**

Potential energy surfaces, force-fields, optimizations, normal mode analysis, predicting thermodynamics, molecular dynamics approaches (basic), empirical force-fields, non bonded interactions, nearest neighbour list, periodic boundary conditions, Ewald summations, simulated annealing, canonical MD simulations,

**2. Sampling, Free Energy Calculations, Rare event simulations:**

Sampling, MD based sampling, MC based sampling, static properties from MD/MC, Bottlenecks of sampling, computing free energy differences, biased sampling, umbrella sampling, metadynamics, parallel tempering, alchemical free energy calculations.

**3. Quantum Mechanical Approaches:**

Basics of molecular orbital theory, Hartree Fock method, and density functional theory, localized molecular orbitals, understanding bonding between atoms in molecules using computation, computing various molecular properties.