Molecular dynamics simulations generate trajectories which depict the system's evolution through time. The results are analyzed both visually (qualitatively) and statistically (quantitatively). Among the most common analytical methods are RMSD, RMSF, and Rgyr, which due to their strictly statistical character inconclusively represent simulation courses. Owing to the complexity of analyzed systems, robust, fast, and intuitive analysis methods are invaluable to both researchers conducting the studies and wider audiences using those results. Clear and intuitive quantitative analyses aid in distinguishing important dana from noise, minimize human error, and facilitate the transfer of information in all stages of research, simplifying communication of scientific findings. In this master's thesis a novel method of molecular dynamics simulation analysis was developed, based on representing trajectories with heatmaps called “Trajectory maps”. This approach offers an intuitive visualization of the entire simulation course, a direct and conclusive comparison of multiple simulation sets, an intuitive and an effective visualization of protein region movements during simulation, etc. The method is designed to complement existing quantitative and qualitative analysis approaches and to combine with them, making it particularly useful to both experienced and new researchers.