CmDock is a software tool developed for performing molecular docking simu-
lations. Due to the possibility of parallel processing, it is particularly suitable
for use on graphics processing units, which allows for faster execution of com-
putationally demanding simulations. Although CmDock includes support for
simulations on graphics accelerators, the current approach is not optimal, as
it does not dynamically adjust the execution parameters depending on the
device. As part of this thesis, a method for automatically selecting optimal
parameters for executing code on a graphics processing unit was added. The
optimization brought noticeable accelerations of docking on graphics process-
ing units, especially for larger complexes and for AMD graphics processing
units.
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