Instructor : Dr. Anand Bharti
Tuesday :- 9:00 AM - 9:50 AM (Room No. 216, Main Building)
Wednesday :- 11:00 AM - 11:50 AM (Room No. 216, Main Building)
Friday :- 11:00 AM - 11:50 AM (Room No. 216, Main Building)
CL 413 FUNDAMENTAL OF MOLECULAR SIMULATION
Credits L:3, T:1, P:0
Class per week 3 hrs
Branch Chemical Engineering
COURSE OBJECTIVES
This course enables the students to:
Understand the basics of statistical mechanics and quantum chemistry.
Explain the working knowledge of Molecular Simulations.
Acquainted a broad overview of various simulation techniques.
Learn current and relevant applications in molecular modelling and simulation.
Develop students' computational programming skills.
COURSE OUTCOMES
After the completion of this course, students will be able to:
Explain the basics of statistical mechanics and molecular simulation.
Apply the Density Functional Theory to Optimize the Geometry of Molecules.
Explain the basics of Monte Carlo/Molecular Dynamics Simulation.
Develop Simple Monte Carlo Simulation Code.
Develop Simple Molecular Dynamics Code.
SYLLABUS
Module I: Ab-initio Methods and Statistical Mechanics:
Ab-initio Methods, The Born-Oppenheimer Approximation, Basis Set, Hartree-Fock Theory, Density Functional Theory, Geometry Optimization. Basics of Statistical Mechanics, Boltzmann Energy Distribution, Partition Functions.
Module II: Monte Carlo Simulation:
Introduction to Monte Carlo, Monte Carlo Integration, Periodic Boundary Conditions, Equilibrations, Monte Carlo Sampling, Markov Process and its applications, Metropolis Sampling, Principles of Detailed balance.
Module III: Monte Carlo Simulation in Various Ensembles:
Simulation Strategy, NVT Ensemble, NPT Ensemble, NVE Ensemble, Grand Canonical Ensemble, Gibbs Ensemble.
Module IV: Molecular Dynamics Simulation:
Basics of Molecular Dynamics Simulation, Force Field, Integrating Algorithms, Periodic Box and Minium Image Convention, Long Range Forces, Non-Bonded Interaction, Simple Molecular Dynamics Program.
Module V: Molecular Dynamics Simulation:
Temperature Control, Pressure Control, Estimation of Pure Component Properties, Radial Distribution Function, Molecular Dynamics Packages.
List of Software which will be used in this course:
Avogadro - advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
GAMESS - The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
MCCCS Towhee The Monte Carlo for Complex Chemical Systems (MCCCS) Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases.
VMD (Visual Molecular Dynamics) - VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
LAMMPS - LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
Text books:
Daan Frenkel, Berend Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2e, Academic Press, New York 2002.
M. P. Allem, D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
Reference books:
Andrew R. Leach, Molecular Modelling: Principles and applications, 2e, Pearson, New Delhi, 2001.
ASSESSMENT
First Quiz 10 Marks (Date: 08.09.2022, Thursday)
Mid Semester Examination 25 Marks (Date: 26.09.2022 onwards)
Second Quiz 10 Marks (Date: 19.10.2022, Wednesday)
Teacher’s Assessment 05 Marks
End Semester Examination 50 Marks (Date: 21.11.2022 onwards)
Course Delivery methods:
• Lecture by use of boards/LCD projectors.
• Tutorials.
• Assignments.
• Seminars/Term Projects.
• Self- learning such as use of NPTEL materials and internets.
Quizzes:
Apart from two compulsory quizzes, there will be several other quizzes at the end of each important topic/each module (Offline/online; 15-30 minutes; weightage: 5 marks ). The quizzes will cover conceptual problems. Material can and will be drawn from the lecture notes.
Midterms and Final:
There will be one mid semester (25 % weightage) and one end semester (50% weightage) exam. Exams will be closed book and closed notes. However, I will provide relevant equations during the exams. The exams will consist of conceptual problems and traditional problems. My intention is to help you develop your problem-solving skills as well as your conceptual understanding of the subject. Material can and will be drawn from the lecture notes.
Week Date Class Day Topic Link
Week 1 10.08.2022 1 Wed Course Introduction and Overview Lecture 1
Week 1 12.08.2022 2 Fri The Dawn of the Quantum Theory Lecture 2
Week 2 16.08.2022 3 Tues The Dawn of the Quantum Theory Lecture 3
Week 2 17.08.2022 4 Wed Schrodinger Wave Equation Lecture 4
Week 3 23.08.2022 5 Tues Particle in a box Lecture 5
Week 3 24.08.2022 6 Wed Particle in a box & Postulates of Quantum Mechanics Lecture 6 Lecture 6
Week 3 26.08.2022 - Fri No Class
Week 4 30.08.2022 7 Tues Postulates of Quantum Mechanics & Helium atom Lecture 7 Lecture 7
Density Functional Theory (DFT) DFT DFT
Basis Sets Basis Sets
Hartree Fock Hartree Fock
Molecular Simulation Molecular Simulation
Monte Carlo Monte Carlo
Monte Carlo Simulation in Various Ensembles