Hands-on Exercise 3 Molecular Dynamics Simulations

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1. General MD Procedure A complete molecular simulation involves 5 steps 1. Model Building • create the molecular model of interest 2. Selection of an appropriate Force Field • simulation results may heavily depend on FF 3. Model Refinement • perform energy minimization to remove VDW repulsions in the initial structure • equilibrate the model at the desired state (T,P or T,V) with sufficient dynamics simulations 4. Dynamics Simulations • production runs 5. Result Analysis • calculation of properties Page 2 stlin@ntu.edu.tw
2. Force Field options in Materials Studio There are two MD programs in Materials Studio 1. Discover 2. Forcite FF selection in Discover: Modules → Discover → Setup FF selection in Forcite: Modules → Forcite → Calculation Page 3 stlin@ntu.edu.tw
Page 1: Computational Chemistry in Chemical
Page 5 and 6: Examine Force Field Parameters Modu
Page 7 and 8: 3. Energy minimization using Forcit
Page 9 and 10: Recap on Energy Minimization (Geome
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)

Hands-on Exercise 3 Molecular Dynamics Simulations

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