Graduate School: Molecular Dynamics & Nanotechnology
(大学院　分子動力学）

Updated: Oct. 21, 2008

Contents

Oct. 7: Maruyama,Introduction (Maruyama)
Oct. 14: Shiomi, Introduction of MD
Oct. 21: Maruyama, Quantum Dynamics & Potential Function
Oct. 28: Maruyama, Potential Functions
Nov. 4: Shiomi, C program and Visualization 1
Nov. 11: Shiomi, C program and Visualization 1
Nov. 18: Shiomi, Tips of MD simulations
Nov. 25: Maruyama, Liquid-Vapor Interface
Dec. 2: Maruyama, Wettability and Nucleation
Dec. 9: Maruyama, Potential for Carbon
Dec. 16: Maruyama, Formation of Fullerene and Carbon Nanotube
Jan. 13: Shiomi, Thermal Conductivity of Carbon Nanotube
Jan. 20: Maruyama, Thermal Boundary Resistance
Jan. 27: Maruyama, Other topics

A reference reading material:

The Manuscript of Molecular Dynamics Simulation.

To download, Login: papers, Password: paper123

Conversion of Energy Units

Scales and Energy (ppt) or in (pdf)

Phase diagram for Lennard-Jones Fluid

Experience of Molecular Dynamics Simulation

1. Download the visualization program
(pvwin.lzh, pvutility.lzh)

DOWN LOAD Visualization Program

2. Download simple MD program to the same folder as
the visualization program.

Simple program (step7b.c, step7b.exe, step.dat)
Simulation conditions are set in step.dat

3. Run step7b.exe (windows).

one of output files, pos.dat is position of molecules.

4. Drag & Drop pos.dat to pvutility.exe. Then, push makepv button.
pos.pv file will be created.

5. Drag & Drop pos.pv file to pvwin.exe

Next Step:

1. Editing step.dat file, you can try different calculations:

2. Download step7b.c, and compile to make step7b.exe

3. Understand step7b.c and modify!

4. ene.dat output file contains energy and pressure data. Plot them.

Powerpoint files of lectures:

1.MD Basics

• Professor Shigeo Maruyama HP

Contact: maruyama [at] photon.t.u-tokyo.ac.jp