2021 Molecular Simulation

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Academic unit or major
Graduate major in Artificial Intelligence
Sekijima Masakazu  Yoshino Ryunosuke  Yasuo Nobuaki 
Class Format
Lecture / Exercise     
Media-enhanced courses
Day/Period(Room No.)
Intensive ()  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
Language used
Access Index

Course description and aims

Molecular simulation with the aid of a supercomputer is an indispensable tool for a life and/or computational science study. This course gives a short overview of molecular orbital calculations by quantum mechanics and molecular dynamics calculations by Newtonian mechanics, followed by an exercise of these calculations mainly targeting biomolecules. Besides, invited speakers from industry provide on-scene use of these technologies.
This course has two aims. The first is to acquire a working knowledge of molecular simulation. The other is to be able to consider using molecular simulation for their studies. These aims would be achieved by experiencing molecular simulations in this course.

Student learning outcomes

1) Be able to imagine how molecules behave in atomistic level by visualization of simulation results.
2) Be able to interpret molecular simulation results.
3) Be able to utilize molecular simulation for their studies.


Molecular orbital calculation, molecular dynamics calculation, docking simulation, Computer-aided drug discovery

Competencies that will be developed

Specialist skills Intercultural skills Communication skills Critical thinking skills Practical and/or problem-solving skills

Class flow

The course is given in a classroom equipped with computers for students. Students spend almost all the time exercising molecular simulation flows, i.e. an input build, calculation, interpretation of results, and visualization.

Course schedule/Required learning

  Course schedule Required learning
Class 1 8/2 Introduction - Overview of molecular simulation Understanding backgrounding theory of molecular simulation and their applications.
Class 2 8/2 What is supercomputer? How to use Linux system Understanding fields where a supercomputer is utilized. An exercise of operating a Linux system.
Class 3 8/25 Molecular orbital calculation 1: Structure optimization, configurational potential energy Conducting structure optimisation and potential energy calculation of a small molecule.
Class 4 8/2 Molecular orbital calculation 2: Infrared spectrum, enthalpy of formation Calculating infrared spectrum and enthalpy of formation of a small molecule. Interpreting calculation results by using the corresponding experimental data.
Class 5 8/3 Molecular orbital calculation 3: Transition state structure, reaction coordinate Predicting reaction coordinate of small molecules, e.g. SN2 and Diels-Alder reactions.
Class 6 8/3 Molecular orbital calculation 4: NMR and UV-vis spectra Calculating NMR and UV-vis spectra of a small molecule and comparing calculated and experimental results.
Class 7 8/3 Molecular dynamics 1: Molecular dynamics of protein molecule I Conducting molecular dynamics simulation of a protein molecule and visualizing the results.
Class 8 8/3 Molecular dynamics 2: Molecular dynamics of protein molecule II Conducting molecular dynamics simulation of a protein-drug complex molecule and visualizing the interaction between protein and drug molecules.
Class 9 8/4 Molecular dynamics 3: Free energy calculation Conducting calculation of the change in binding free energy of protein drug molecules upon mutations in the protein. Calculating solvation free energy of small molecules.
Class 10 8/4 Molecular dynamics 4: Exploration of free energy surface with the extended sampling method Conducting free energy calculation of a molecule with an enhanced sampling method and visualizing results.
Class 11 8/4 Computer-aided drug discovery 1: Ligand-based method Predicting potential inhibitors of a target biomolecule based on known inhibitors’ information.
Class 12 8/5 Computer-aided drug discovery 2: Structure-based method, docking simulation Predicting potential inhibitors of a target biomolecule based on a structure of the target molecule.
Class 13 8/5 Computer-aided drug discovery 3:Project based learning for drug discovery (1) Designing a plan for a proposal of potential inhibitors against a designated target biomolecule by combining tools provided in this course.
Class 14 8/5 Computer-aided drug discovery 4:Project based learning for drug discovery (2) Designing a plan for a proposal of potential inhibitors against a designated target biomolecule by combining tools provided in this course.


No textbook is set.

Reference books, course materials, etc.

Materials used in every lesson are handed out in the class.

Assessment criteria and methods

Reports for relevant simulation results, interpretation of the results, and invited talks are taken into account.

Related courses

  • LST.A211 : Physical Chemistry III
  • CSC.T353 : Biological Data Analysis
  • ART.T543 : Bioimformatics

Prerequisites (i.e., required knowledge, skills, courses, etc.)

No prerequisites.


It will be held as an intensive lecture on the following schedule.
8/2 - 28 8:50-
This lecture will be held at Computer Network Exercise Room (Ookayama Campus).
Lecture rooms are possibly subject to change.

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