一、課程說明
Course Description Basic to Advanced Simulation Techniques; CONFFERED IN ENGLISH
二、指定用書
Text Books Molecular Modeling - Principles and Applications, by Andrew R Leach
三、參考書籍
References “Normal Mode Analysis”by Qiang Cui & Ivet Bahar
“Coarse-Graining of Condensed Phase and Biomolecular Systems”by Gregory A Voth
四、教學方式
Teaching Method Lectures by teacher and students plus hands-on practice in programming and using
computer software
五、教學進度
Syllabus MD simulations
Interactions between atoms (forcefields)
MD simulations I - Basics
MD simulations II – paper discussions on Ewalds Methods
MD simulations II – paper discussions on temperature control
MD simulations IV – paper discussions on pressure control #
MD simulations V – paper discussions on surface tension control
MD simulations VI – paper discussions on target MD #
MD simulations VII – paper discussions on steered MD
MD simulations VIII – paper discussions on Replica Exchange Simulations #
MD simulations IX – paper discussions on Gibbs Free Energy Calculations #
MD simulations X – paper discussions on coarse-grained MD simulations #
Normal Mode Analysis
Normal Mode Analysis I - Basics
Normal Mode Analysis II - ANM
Normal Mode Analysis III - GNM
Normal Mode Analysis IV - EPIRM
六、成績考核
Evaluation Presentation (100%)