Hands-on Exercise 3 Molecular Dynamics Simulations
Hands-on Exercise 3 Molecular Dynamics Simulations Hands-on Exercise 3 Molecular Dynamics Simulations
4. Dynamics Simulation using Forcite Modules → Forcite → Calculation → Setup → Dynamics ensemble initial atom velocity dynamic temperature dynamic pressure integration step simulation length output frequency Page 10 T control method P control method stlin@ntu.edu.tw
Recap on Dynamics Simulations 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. Make sure the structure is stable (either previously energy minimized or having dynamics simulation performed) 3. Set simulation parameters (ensemble, initial velocity, dynamics temperature and thermostat, pressure and barostat, integration step, simulation length, output property and frequency) Page 11 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 and 8: 3. Energy minimization using Forcit
- Page 9: Recap on Energy Minimization (Geome
- 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)
4. <strong>Dynamics</strong> Simulati<strong>on</strong> using Forcite<br />
Modules → Forcite → Calculati<strong>on</strong> → Setup → <strong>Dynamics</strong><br />
ensemble<br />
initial atom velocity<br />
dynamic temperature<br />
dynamic pressure<br />
integrati<strong>on</strong> step<br />
simulati<strong>on</strong> length<br />
output frequency<br />
Page 10<br />
T c<strong>on</strong>trol method<br />
P c<strong>on</strong>trol method<br />
stlin@ntu.edu.tw
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