Computational Chemistry and Classical Molecular Dynamics
ABOUT THE COURSE:
This course introduces learners to elementary programming and numerical
methods that are useful to solve problems in chemistry. These methods are useful for understanding
molecular structures as well as condensed media such as liquids and solutions. For rapid calculations,
the public domain software Scilab is used and applications to several numerical methods relevant to
chemistry are discussed. Basic mathematical background is provided wherever necessary. Classical
molecular dynamics simulations are performed using the public domain software gromacs. Installation
procedures as well explicit calculations are demonstrated. All these calculations can be performed on a
personal computer.
Important For Certification/Credit Transfer:
Weekly Assignments and Discussion Forum can be accessed ONLY by enrolling here
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Note: Content is Free!
All content including discussion forum and assignments, is free
Final Exam (in-person, invigilated, currently conducted in India) is mandatory for Certification and has INR Rs. 1100 as exam fee
INTENDED AUDIENCE: All chemistry students
CORE/ELECTIVE: Both
UG/PG: UG and PG
PREREQUISITES: Good high school education. Thermodynamics in Bachelors courses will help
INDUSTRY SUPPORT: Any pharmaceutical company will find this useful
727 students have enrolled already!!
ABOUT THE INSTRUCTOR:
Ph. D in theoretical chemistry /chemical physics from Stony Brook University, 1981. Have taught
physical/theoretical/computational chemistry and researched in these areas for nearly 40 years
COURSE LAYOUT:
Week 1 : General Introduction and course outline, Algorithms Simple programs and the sine function, Flow charts, recursion relations and convergence and do loops, Branching and if statement. Solving a quadratic equation, Quadratic equation, dimension statement, Reading and writing from files Week 2 : Execution of simple programs-1, Execution of programs-2, Functions and subroutines-1, Functions and subroutines-2, Newton Raphson method, Interpolation 1. Week 3 : Program execution 3, Program execution 4, Matrix methods 1, Matrix methods 2, Matrix methods 3, Differential Equations Week 4 : Integration, Curve fitting-1, Curve Fitting 2, Scilab 1, Scilab 2, Scilab 4 Week 5 : Scilab 4, Classical MD -1, Classical MD -2, Classical MD 3, Classical MD 4, Plotting PEs Week 6 : Gromacs files-1, Gromacs files-2, Gromacs commands-1, Gromacs Commands-2, Gromacs Installation 1, Execution for Argon and water
Week 7 : Results for liquid argon, Water simullations 1, Water simulations 2, Liquid mixture simulation, Calculation of the potential force (PMF), Computing the PMF
Week 8 : Correlation functions-1,Correlation functions-2, Free energy of solvation, Computing the free energy, Protein dynamics, Lysozyme simulation.
SUGGESTED READING MATERIALS:
NPTEL web course on computational chemistry
CERTIFICATION EXAM :
The exam is optional for a fee.
Date and Time of Exam: October 7, 2018 (Sunday):
Time of Exams: Morning session 9am to 12 noon; Afternoon session: 2pm to 5pm.
Exam for this Course will be available in both morning & afternoon sessions.
Registration url: Announcements will be made when the registration form is open for registrations.
The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published.
CERTIFICATE:
Final score will be calculated as : 25% assignment score + 75% final exam score
25% assignment score is calculated as 25% of average of Best 6 out of 8 assignments
E-Certificate will be given to those who register and write the exam and score greater than or equal to 40% final score. Certificate will have your name, photograph and the score in the final exam with the breakup.It will have the logos of NPTEL and IIT Bombay.It will be e-verifiable at http://nptel.ac.in/noc/
