VIAMD is developed in our group and allows a visual exploration of large-scale spatio-temporal molecular dynamics simulation data. VIAMD can be seen as an optimization to the common MD-analysis workflow, which tightly couples the three main tools of MD-analysis: visualization, property computation and plotting. By placing the three tools within the same application we are able to leverage synergies formed by the tight coupling. Examples of such synergies is the interactivity of clicking on temporally plotted property to go to that point in time to immediately correlate the value to the spatial conformation of the system. Another example is the ability to directly declare derived properties from spatial selections in the visualization and to visualize user declared properties within the visualization to aid the user in asserting the operation and structures involved.
VIAMD is in constant development and several directions could be taken depending on the interest of the applicant, for example:
- Analysis of multiple trajectories
- Coupling of VIAMD software to a Molecular Dynamics engine
- Interactive Molecular Dynamic Simulation with haptic
- Rendering of surface based on a subset of atoms