Simulation or Run Time

The simulation or run time includes time for the system to equilibrate at the simulation temperature plus the time for data collection, while the trajectory evolves. Simulation times depend on the time scale of the property you are investigating. 

Example For a medium-sized molecule in the gas phase, with vibrations larger than 50 cm a trajectory of only 10 ps should be adequate to explore motions due to vibrations. 

Eample For protein molecules with motions occurring at a frequency of about 1 cm the vibrational period is about 30 ps. Clearly, simulations of hundreds of picoseconds are necessary to probe adequately the motions of this system. 

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