Hands-on Exercise 3 Molecular Dynamics Simulations

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)
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