Let’s draw a line. Across the calendar, I mean. Let’s all pledge that from today on we’re going to give honest accounting of the uncertainty in our data. I mean ‘honest’ in the sense that if someone tried to reproduce our data in the future, their confidence interval and ours would overlap.

There are a few conceptual issues to address up front. Let’s set up our discussion in terms of some variable which we measure in a molecular dynamics (MD) simulation at successive configurations: , , , and so on. Regardless of the length of our simulation, we can measure the average of all the values . We can also calculate the standard deviation σ of these values in the usual way as the square root of the variance. Both of these quantities will approach their “true” values (based on the simulation protocol) with enough sampling – with large enough .