FAQ

How to cite?

See How to cite section on the main page.

Is CaverDock execution deterministic?

In the default settings, it is not deterministic (i.e., re-executing CaverDock may result in different trajectories). There is, however, a way how to make CaverDock deterministic. It must be executed in two processes only (using mpirun -np 2), and the random number generator must be set to a constant seed (using --seed x, where x is any number, which must be the same for all deterministic executions). Please note that when CaverDock is executed only for single docking (possibly with restraints), setting a constant seed is sufficient.

Why does CaverDock return two types of energy?

A heuristics drives the CaverDock computation of an upper-bound trajectory. It means that CaverDock cannot guarantee that the contiguous trajectory is optimal. Thus, CaverDock is computing also a lower-bound trajectory: a scenario, which can be unrealistically optimistic due to non-continuities in the trajectory. The real energy (with respect to the given force-field and the geometry of the input molecules) is at most as high as the energy of the upper-bound trajectory and at least as low as the energy of the lower-bound trajectory.