一、課程說明(Course Desc<x>ription)
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<br>In this course, I will teach molecular dynamics simulations to students. 
<br>Capabilities of programming and running programs are prerequisites for this 
<br>course. Knowledge about numerical analysis, classical mechanics and
<br>statistical mechanics in very helpful in understanding the techniques and
<br>methods of molecular dynamics simulations.
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<br>二、指定用書(Text Books)
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<br>None
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<br>三、參考書籍(References)
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<br>1. Rapaport, the Art of Molecular Dynamics Simulation, 2nd edition, 
<br>Cambridge 2004
<br>2. Haile, Molecular Dynamics Simulation -- elementary methods, Wiley 1992
<br>3. Allen and Tildesley, Computer Simulation of Liquids, Oxford 1987
<br>4. Frenkel and Smit, Understanding Molecular Simulation -- from Algorithms 
<br>to Applications, 2nd edition, Academic Press 2002
<br>5. Tuckerman, Statistical mechanics: Theory and molecular simulation, Oxford 
<br>2010 
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<br>四、教學方式(Teaching Method)
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<br>three lecture hours per week. 
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<br>Note: this is not an "experimental" or "practical" course. 
<br>There will be no class to teach students how to do programming or running 
<br>simulations. However, programming and running simulations will be a part of 
<br>student's home works.
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<br>五、教學進度(Syllabus)
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<br>1.Introduction (week 1)
<br>2.Basic molecular dynamics (week 2)
<br>3.Integration methods: Euler’s method, Runge-Kutta method, predictor-
<br>corrector method, Verlet algorithm; Interaction computations: neighbor-list 
<br>method, cell subdivision (week 3 & 4)
<br>4. Alternative ensembles: NVT, NPT (week 5 & 6)
<br>5.Statistical properties: RDF, heat capacity, chemical potential, entropy 
<br>(week 7)
<br>6.Dynamical properties: transport coefficients, dynamic structure (week 8)
<br>7.Long-range interactions: Ewald summation  (week 9 & 10)
<br>8.Geometric constraints: Shake and Rattle algorithms (week 11)
<br>9.Rigid molecules: quaternions  (week 12)
<br>10.Many-body interactions: three-body forces, EAM (week 13)
<br>11.Multiple time step scheme: rRESPA (week 14&15)
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<br>六、成績考核(Evaluation)
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<br>Homework     30%
<br>Midterm exam 35%
<br>Final exam   35%
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<br>七、可連結之網頁位址
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<br>For more information, please refer to
<br>http://mx.nthu.edu.tw/~pyhsiao/teaching.htm
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