Tutorials#
Step-by-step lessons that take you from zero to a working result. For working with the Molecule class itself (loading structures, atom selection, trajectories, visualization) see the moleculekit tutorials.
System building#
The headline capability. Each tutorial walks through building a real, simulation-ready system end-to-end - protein preparation, segmentation, ligand placement, membrane embedding, and parameter assignment under CHARMM / AMBER. The system-building overview lays out the full feature set, including non-canonical amino acids, stapled peptides, isopeptides, and disulfide handling.
Running MD simulations#
Drive a built system through equilibration and production with the ACEMD MD engine. The tutorial uses the canonical Trp-cage build as input, walks the setup_equilibration → acemd → setup_production → acemd chain, and ends with the trajectory that downstream MSM analysis consumes.
MSM analysis#
Two end-to-end MSM analyses on real systems - benchmark trypsin/benzamidine and villin folding. Each tutorial walks the full simulation-list → projection → clustering → model → kinetics pipeline. The MSM workflow concept page sketches that pipeline before you start.
Adaptive sampling#
Multi-epoch campaigns whose next starting frames are picked from an on-the-fly MSM. The adaptive sampling concept page explains the rationale.