From Interactive to Immersive Molecular Dynamics

Abstract

Molecular Dynamics simulations are nowadays routinely used to complement experimental studies and overcome some of their limitations. In particular, current experimental techniques do not allow to directly observe the full dynamics of a macromolecule at atomic detail. Molecular simulation engines provide time-dependent atomic positions, velocities and system energies according to biophysical models. Many molecular simulation engines can now compute a molecular dynamics trajectory of interesting biological systems in interactive time. This progress has lead to a new approach called Interactive Molecular Dynamics. It allows the user to control and visualise a molecular simulation in progress. We have developed a generic library, called MDDriver, in order to facilitate the implementation of such interactive simulations. It allows one to easily create a network connection between a molecular user interface and a physically-based simulation. We use this library in order to study a biomolecular system, simulated by various interaction-enabled molecular engines and models. We use a classical molecular visualisation tool and a haptic device to control the dynamic behavior of the molecule. This approach provides encouraging results for interacting with a biomolecule and understanding its dynamics. Starting from this initial success, we decided to use Virtual Reality (VR) functionalities more intensively, by designing a VR framework dedicated to immersive and interactive molecular simulations. This framework is based on MDDriver, on the visualisation toolkit VTK, and on the vtkVRPN library, which encapsulates the VRPN library into VTK.