How-to guides#
Task-oriented recipes. Each page solves one concrete problem; pick the one matching your situation. Molecule-level recipes (reading, selection, wrapping, projections, …) live in moleculekit’s how-to guides - the pages here cover the HTMD layer above that (system building, simulation orchestration, MSM analysis).
System building#
Membranes#
Adaptive sampling#
MSM analysis#
- How to build a simlist from a non-standard directory layout
- How to filter trajectories with simfilter
- How to drop bad trajectories from an MSM dataset
- How to choose a featurization with a VAMP-2 score
- How to bootstrap an MSM for error bars on timescales
- How to read off and interpret an implied-timescales plot
- How to plot a free-energy surface from an MSM
- How to extract a representative structure per macrostate