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Course Description

This course is on methods for molecular simulations.

Instructor: Dr. Nisanth N. Nair (Email:, 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



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.