Determining the anchor points for the host-guest complex is the first step towards milestoning simulations in the SEEKR2 framework. We first choose an appropriate collective variable (CV) to determine the anchor points that could describe the receptor-ligand binding and unbinding dynamics. In the case of the host-guest complex, we choose the distance between the center of mass (COM) of the receptor (β-cyclodextrin) and the ligand as the CV to determine the anchor points. The anchor points, therefore, lie on a line composed of the COM-COM distance. Once the anchor points are determined, we define concentric spherical milestones around the receptor-ligand binding site where the concentric radii are midpoints of any two consecutive anchor points. These milestones will act as reference points during the simulation. We then use steered MD (SMD) to slowly pull the ligand away from the binding site with a harmonic restraint and save the trajectory snapshots as it crosses the anchor point while slowly moving out of the binding pocket. Once the ligand is pulled out completely, we have the saved structure files, which will be used to create a SEEKR2 file tree where SEEKR2 simulations will occur. Holo insertion by directed restraints (HIDR), a computational method employed in the SEEKR2 framework, utilizes one or more initial configurations alongside a SEEKR2 input XML file, pulls the system towards all the anchors present in the SEEKR2 framework until starting structures exist in all of them. The HIDR algorithm employs SMD simulations to accomplish this. By default, HIDR SMD simulations move the system towards each anchor at an approximate 0.01 nm/ns speed. This speed is designated to let the system reach each anchor within a reasonable time frame while avoiding excessive perturbations to the system. However, the speed can be adjusted using the -v argument. For instance, if the user desires to perform SMD simulations ten times faster (thus completing in one-tenth of the time), the speed can be set to 0. python ∼/seekr2/seekr2/run.py any \ SEEKR_simulation/model.xml