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Course10410109541 lectures

Computational Chemistry and Classical Molecular Dynamics

Prof. B. L. Tembe · IIT Bombay

Start with lecture 1 At NPTEL

Lectures

Week 1 : Elementary Programming and Linux commands

  1. Lecture 1 : Introduction to Computational Chemistry Video
  2. Lecture 2 : Writing Simple Programs: Compilation and Execution Video
  3. Lecture 3 : Programming Techniques-1: Evaluating the sine function Video
  4. Lecture 4 : Programming Techniques 2: Do loops and if statements Video
  5. Lecture 5 : Programming Techniques 3. Roots of a quadratic equation and arrays Video

Week 2 : Programming, Array Variables, Subroutines and Numerical methods

  1. Lecture 6 : Programming Techniques 4. Arrays and matrices Video
  2. Lecture 7 : Practical Session of Programming 1 Video
  3. Lecture 8 : Programming Techniques 5. Formats, Functions and Subroutines Video
  4. Lecture 9 : Programming Techniques 6. Functions and Subroutines, arranging numbers in as ascending order Video
  5. Lecture 10 : Programming Techniques 7. Functions and Subroutines, and the common statement Video

Week 3 : Programming, Functions and Subroutines, Numerical Methods: Interpolation and Matrix operations

  1. Lecture 11 : Numerical Methods. Analysis of errors Video
  2. Lecture 12 : Practical Session on Programming 2: The exponential function Video
  3. Lecture 13 : Practical Session on Programming 3: Functions and Subroutines Video
  4. Lecture 14 : Interpolation Methods 1 Video
  5. Lecture 15 : Interpolation Methods 2: Newton's and Lagrange Interpolation Video

Week 4 : Matrix Inversion, Diagonalization andCurve Fitting

  1. Lecture 16 : Errors in interpolation, Matrix operations Video
  2. Lecture 17 : Gauss elimination method for matrix inversion Video
  3. Lecture 18 : Matrix diagonalization, Similarity transformations Video
  4. Lecture 19 : Matrix inversion, Matrix diagonalization Video
  5. Lecture 20 : Curve fitting, Newton Raphson method Video

Week 5 : Random Numbers, Numerical Integration and Introduction to SCILAB

  1. Lecture 21 : Random numbers, Numerical integration using Simpson's rule Video
  2. Lecture 22 : Numerical Integration and Differential Equations. Video
  3. Lecture 23 : Practical Session on Programming 3: Random numbers, Simpson's rule; Introduction to Scilab Video
  4. Lecture 24 : Scilab-2: Matrix equations and Roots of Polynomials Video
  5. Lecture 25 : Scilab-3: Functions, Integrals, Differential Equations and graphs Video

Week 6 : Scilab Programming: Curve Fitting, Graphics, Integral Transforms and Introduction to Molecular Dynamics

  1. Lecture 26 : Scilab-4: Curve Fitting and Execution of Scilab programs Video
  2. Lecture 27 : Scilab-5: Legendre polynomials, Multiple plots and Curve fitting Video
  3. Lecture 28 : Scilab-6: Integral Transforms; Introduction to Molecular Dynamics (MD) Video
  4. Lecture 29 : Classical Molecular Dynamics - 2, Force Fields and Equations of Motion Video
  5. Lecture 30 : Classical Molecular Dynamics - 3, Force Fields and MD Algorithms Video

Week 7 : Molecular Dynamics Algorithms, Execution of Programs for liquid Argon and Introduction to GROMACS

  1. Lecture 31 : Classical MD-4 Thermodynamic Properties and Distribution Functions. Video
  2. Lecture 32 : Classical MD-5, Execution of programs on liquid argon Video
  3. Lecture 33 : Molecular Dynamics using Gromacs-1 Video
  4. Lecture 34 : Molecular Dynamics using Gromacs-2 Simulating Liquid Argon Video
  5. Lecture 35 : Molecular Dynamics using Gromacs-3: Installing Gromacs Video

Week 8 : GROMACS Input Files, simulations of Liquid water, water methanol mixtures, s-peptide and free energy of…

  1. Lecture 36 : Molecular Dynamics using Gromacs-4: Liquid Water: Input Files Video
  2. Lecture 37 : Molecular Dynamics using Gromacs-5: Liquid Water: Analysis of Results Video
  3. Lecture 38 : Molecular Dynamics using Gromacs-6: Mixture of Water and Methanol Video
  4. Lecture 39 : Molecular Dynamics using Gromacs-7: Gromacs Installation Video
  5. Lecture 40 : Molecular Dynamics using Gromacs-38 Simulation of s-peptide Video
  6. Lecture 41 : Molecular Dynamics using Gromacs-9: Free Energy of Solvation of Methane, Concluding remarks Video

Syllabus and materials

At NPTEL, as the course publishes them.

Credits and licence

Institution
IIT Bombay
Department
Chemistry and Biochemistry
Teacher
Prof. B. L. Tembe
Level
Undergraduate
Language
English
Subjects
Chemistry
Source
NPTEL
Licence
CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
Attribution
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