Nowadays, biologists deal with gigabytes of data as the results of molecular dynamics simulation. To understand and interpret the molecular dynamics results and to come up with new hypotheses the user often needs visualization and querying tools to be interactively involved in the process of visual data mining and querying of the spatio-temporal data. In this paper, we propose a novel visual query system for visualization of molecular dynamics simulation results and visual querying. The system design and its implementation are described. We propose specific visual queries for visual data analysis in molecular dynamics. The proposed visual query system is unique and allows us to formulate spatio-temporal queries that cannot be implemented directly using any available spatio-temporal database system and/or molecular visualization program. This paper is the result of collaborative research and graduate study.