I am a beginner in MD simulation, my question is what occurs if instead of 0.5 femto-second I choose 5 ft as time step of my simulation I am doing MD with protein.
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1 Answer
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The appropriate timestep is determined by the interactions that are present in your simulation. For example, if you have a spring with spring constant $k$ attached to a particle of mass $m$, your time step must be significantly smaller than the characteristic time of the oscillator, $\tau = \sqrt{m/k}$. You therefore have to think about the shortest characteristic timescales that your simulation contains. What happens at any particular value of the time step cannot be answered in general.
