Novel insight on molecular dynamics trajectories : local equilibrium viewed by kappa-segmentation

Molecular dynamics (MD) simulations can produce nowadays huge amount of data using high-throughput CPU/GPU clusters. However, the systematic and routine use of MD simulations for a study of the large molecules of real biological systems is still considerably impeded by a lack of adequate modelling. This leads to a limited understanding of the produced highly complex signals that emerge at the level of the relevant subsystems for various time scales. We will present here an ongoing work towards the dynamics modelling and detection of local equilibrium for relevant subsystems compatible with the usual practice of MD and aiming at avoiding the detection of spurious artefactual local equilibrated states. Such well characterized local equilibrium would be basic descriptive atoms extracted from various MD trajectories.