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paper/basic_training.tex

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@@ -1191,7 +1191,7 @@ \section{Should you run MD?}
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As noted above, the frequency of the fastest vibrational motions in a system of interest sets a fundamental limit on the timestep which, given fixed computational resources, sets a limit on how much simulation time can be covered with any reasonable amount of computer time.
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Thus, as noted in Section~\ref{sec:intro}, the longest all-atom MD simulations are on the microsecond to millisecond timescale.
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This means that if your system is complex and answering your questions will require sampling critical events that have a timescale of seconds or longer, MD will not be the right tool for the job.
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You could invest a huge amount of effort running a MD simulations and find that these do nothing whatsoever to address your questions.
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You could invest a huge amount of effort running MD simulations and find that these do nothing whatsoever to address your questions.
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Ideally, you should have some information before beginning that the relevant timescales for your system might be accessible given the amount of MD you can afford to run, or you could plan a set of exploratory MD simulations to assess feasibility.
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But do not simply plunge in and attempt to run simulations until you find the answers to your questions, as the required timescales could end up being orders of magnitude longer than what you can afford to spend.

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