Hands-on Exercise 3 Molecular Dynamics Simulations
Hands-on Exercise 3 Molecular Dynamics Simulations Hands-on Exercise 3 Molecular Dynamics Simulations
Define Motion Groups Modify → Motion Groups Note: Use undo or delete to remove Motion Groups Page 8 stlin@ntu.edu.tw
Recap on Energy Minimization (Geometry Optimization) 1. Choose a force field (check atom type, atomic charges) [Note that it is important to check if net charge of your model is zero] 2. Choose convergence tolerance (when to stop the minimization) and maximum iteration steps (stop no mater what) 3. Whether to optimize the cell parameters (cell lengths and angles) 4. Whether to keep some molecules rigid during the geometry optimization Page 9 stlin@ntu.edu.tw
- Page 1 and 2: Computational Chemistry in Chemical
- Page 3 and 4: 2. Force Field options in Materials
- Page 5 and 6: Examine Force Field Parameters Modu
- Page 7: 3. Energy minimization using Forcit
- Page 11 and 12: Recap on Dynamics Simulations 1. Ch
- Page 13 and 14: 5. Analysis of MD Results Basic pro
- Page 15 and 16: Advanced Analysis Modules → Forci
- Page 17: 7. Create Animation (Making movies)
Recap <strong>on</strong> Energy Minimizati<strong>on</strong> (Geometry Optimizati<strong>on</strong>)<br />
1. Choose a force field (check atom type, atomic charges)<br />
[Note that it is important to check if net charge of your<br />
model is zero]<br />
2. Choose c<strong>on</strong>vergence tolerance (when to stop the<br />
minimizati<strong>on</strong>) and maximum iterati<strong>on</strong> steps (stop no<br />
mater what)<br />
3. Whether to optimize the cell parameters (cell lengths and<br />
angles)<br />
4. Whether to keep some molecules rigid during the<br />
geometry optimizati<strong>on</strong><br />
Page 9<br />
stlin@ntu.edu.tw
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