********************3rd FCS School****************

Title : Introduction to Molecular Simulation

Speaker : Dr. Vladislav Vassiliev *
          Dr. Ivan Rostov *
          Dr. Roger Amos *
          Dr. Rika Kobayashi *
          Dr. Norio Takenaka $
          Dr. Masayoshi Takayanagi $
          Dr. Ikuo Kurisaki $

Affiliation : * The Australian National University
              $ Nagoya University

Date : Tues. Jun. 23rd, 10:00 am 
       (Almost seven hours)

Place : ES hall, Nagoya University

Contents :
Abstract：
In this seminar, we learn how to use AMBER, a 
widely used molecular dynamics (MD) simulation 
program package for chemical species and bio-
molecules. The curriculum includes both their 
basic and advanced usages. We start from the 
basic setup and execution of MD simulations. 
Then, we introduce advanced usages, the binding 
free energy calculations and the hybrid 
simulations with molecular mechanics (MM) and 
quantum mechanics (QM), i.e., QM/MM method.

Program 

Jun.23 (Tue.)
10:00-10:30  Theoretical Background of Molecular 
             Simulations
	Norio Takenaka
(Break 10 min.)
10:30-11:10  Introduction of Molecular Simulation 
             Using AMBER (1)
	Ikuo Kurisaki
(Break 10 min.)
11:20-12:00  Introduction of Molecular Simulation 
             Using AMBER (2)
	Masayoshi Takayanagi

Lunch

13:10-14:25  Evaluating Free Energies of Binding 
             Using Amber: The MM-PBSA Approach
	Vladislav Vassiliev
(Break 10 min.)
14:35-15:50  A Hybrid QM/MM Approach and its 
             Implementation in Amber
	Vladislav Vassiliev
(Break 10 min.)
16:00-17:00  Introduction to Application Research 
             with Computational Quantum Chemistry
	Rika Kobayashi

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