Practicalities on using MD

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Presentation transcript:

Practicalities on using MD Geometry constraints: Z-matrix Equilibration of MD Restart of phonon calculations

Z-Matrix coordinate format Internal coordinates: Molecules represented by : Bond lengths i Bending angles i Dihedral angles i  

Z-Matrix Allows for mixing of generalised and Cartesian coordinates: Useful for constraint relaxations Explore the PES by using A relevant coordinate: Useful for estimating barriers

Z-matrix Symbol Section ------- Variables zm1 2.55000000000000 Constants cc 1.41700000000000 ccc 120.000000000000 ch 1.11200000000000 cch 120.000000000000 ------------ End of Z-matrix Information

Equilibration of MD

Moving -windows Divide the trajectories in overlapping windows of 7.5 ps length and 2 ps interval Moving -windows

Output files SystemLabel.XV Stores coordinates and Velocities, necessary for restarts (keep always a backup copy!!) SystemLabel.MDE SystemLabel.MD : Saves positions and Velocities for each time frame, formatted.

Phonon Calculations Easy to parallelize: Each displacement is independent of others. We can parallelize by atoms. Care is needed when reassembling the .FC files. If calculation crashes we can restart it without loosing information, but doing it with care.