Molecular dynamic simulations are computer simulations of the physical movements of atoms and molecules and the interactions between them. They are used in various areas such as physics, chemistry, material sciences and modelling of biomolecules.
In drug design, simulations of the molecular dynamic predict the type of bond and the affinity of the combination of a small molecule (the drug) with a biomolecule (protein). The result, if successful, is a drug that has therapeutic benefits for the patient.
The ViRVIG group has worked on molecular visualisation to address various aspects, such as the generation of realistic lighting in models of very large molecules or the visualisation of extremely long simulations of molecular dynamics. To meet these objectives, the group has developed tools for visual exploration of molecular simulations, which has facilitated the analysis and saved time, particularly in the visualisation of trajectories.
An example of applications are compact molecular simulations that abstract a 3D structure into a 2D design. Based on a web application that offers rapid, intuitive exploration of complete simulations, many physical properties are represented such as energy, index of flow of waste products or hydrogen bridges, among others.
A second example tackles the challenge of exploring extremely large molecular trajectories (of hundreds of thousands of steps). To achieve this, simulation data are analysed automatically, and relevant characteristics are extracted. Subsequently, through a set of coordinated views in 2D and 3D, an application is obtained that facilitates the progressive exploration of molecular simulation in a very efficient, intuitive way. The result is a graphic application that could be executed on a PC with a graphics card.
The developments have been made in collaboration with the Barcelona Supercomuting Center (BSC), the University of Ulm, Masaryk University, the Czech Republic and the Laboratory of Loschmidt in Masaryk University.