Proving competing pathways in Protein-B for analysis in variable water mass simulations

Proteins operate by folding and unfolding between a structure specific to that protein and to being stretched out. This folded structured state is known as the native structure and folding to and from this state is how the body operates. The protein can fold in multiple different ways to reach the native structure and the order of folds that occur are called folding pathways. Competing pathways are when certain pathways appear a significant amount compared to others and have a reasonable chance of appearing in a folding event. The objective of proving competing pathways is providing variables to observe during varying water mass simulations. The goal of the project is performing simulations of Protein-B trajectories at varying water mass to observe whether the varied water mass would affect appearance rate of various, competing, folding pathways. Appearance rate is defined as the measurement of amount of appearances certain pathway defining features occur over the course of a whole trajectory and comparing results in a before and after situation.