We have a vision of MD simulations as consisting of an initial equilibration phase, during which system variables relax to "realistic" values, followed by the "production" phase from which valid estimates of features or behaviours of interest can be extracted. So how do we decide when an MD simulation is long enough that it is equilibrated, and data collection can begin?
This workshop looks at one of the most common methods for assessing equilibration: the calculation of RMSDs. It may be a common approach, but is it a good one? Maybe not.
A basic knowledge of Python and MD simulation methods
A Jupyter notebook and associated data files
Please direct all comments and queries to Charlie Laughton