examples of bad practice should be removed from sample scripts

[kosovan]

The following issues should be removed from all sample scripts (if still present).
Otherwise, beginners copy the sample scripts, adopt them for their system, and use the bad practice in their production scripts.

• The observable time series should be saved in an observable file and processed independently after the simulation, not on the fly.
• The equilibration time time is not known beforehand. Therefore, full observable time series should be saved.
• Running a set of simulations at different conditions (e.g. different pH values) within a single script is not advisable
• The nomenclature step and sample is used ambiguously and inconsistently
• All independent input parameters should be set within a single block of code, not scattered through the whole script
• Post-processing the time series, merging and plotting the results from multiple simulations should be a separate example