This application concerns the coupling of a molecular dynamics (MD) simulation to a virtual reality system. Molecular modeling tools are essential to design and study new molecules. For example, when steering a molecular dynamics simulation, the user can express external forces to help the system to overcome energy barriers, or can help in the search for likely geometric configurations in docking problems. VR allows the scientist to gain a deeper understanding of the complex conformations in 3D. Moreover, modifying 3D structures or expressing forces is intrinsically a 3D process, for which the use of a immersive virtual environment is a perfect match.

As a feasibility study (and for later experiments on interaction and measurement), we wrapped the molecular dynamics NAMD simulation and visualized it in a VR environment. Our current implementation allows a remote simulation running on the DAS parallel cluster computer to be visualized in the CAVE. The input parameters we selected are the name of the molecule on which the simulation will be applied, the number of time steps of the simulation, and the temperature. It corresponds to the minimal set of parameters among the large possibilities of NAMD. We did not implement the interactive parameter selection yet, but parameters can be modified at starting time. As output of the simulation, we use the PDB description files produced as intermediate result during the execution. These files, which contain the position and velocity of all the atoms, are read by the proxy process and sent continuously to the visualization, showing the dynamic of the molecule. Several classic molecule representations are available.

The coupling of MD simulation to visualization has already been done before, but always by modifying source code. Using CAVEStudy, we were able to very quickly couple NAMD to our virtual environment. With CAVEStudy, we can easily switch between several simulation packages. Furthermore, to steer such a simulation adequately, 3D forces should be expressed, which can efficiently be done in a 3D VR environment implemented by CAVEStudy.