Folding/Aggregation Event

Many of the simulations run by Pande Group study protein folding/misfolding or aggregation/disaggregation. When a simulation encounters a state in which the protein begins to fold or aggregate, all the atoms in the system move closer together. This makes calculating the forces exerted by the atoms on each other much more complex and time-consuming compared to when the atoms are further apart. Most of the time during the simulation (and thus in most WUs) the protein is in a relaxed state, which changes little over the course of the simulation. However the process of folding occurs very quickly, the protein literally "snaps" into position. When this occurs, sections of the proteins may pass very close to each other, complicating the force calculations. The extra complexity of the calculations means that frames where this is taking place take longer to process than others. This phenomenon is referred to as a Folding Event. Sometimes only a couple of frames in the WU increase in complexity, on other occasions it happens to all frames beyond a certain point. Aggregation events follow the same principle, except that it is whole proteins moving closer together rather than sections of a single proteins (inter as opposed to intra).

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