These scripts were used for various types of analysis of the data. The scripts follow below with a brief description of what each was used for.
Bi to Mono dentate - this file mutates an ion conjugated by acetate from the bi to the mono and finally to the unbound state, to approximate the interaction energy between ion and acid.
Equilibration - This allows the systems to undergo free dynamics for a time, to allow analysis of the average state of the system in free motion.
Minimization - This minimizes the structure given, allowing analysis of the minimum potential energy state of the system.
Simulated Annealing - This is a more effective minimization algorithm, allowing free dynamics between steps of minimization to avoid local potential energy wells.
Decomposition - This allows the decomposition of the system potential energy into various components.
Constrained Perturbation - This allows a perturbation with the acid group restricted to the monodentate state, gauging the effects of acid coordination on perturbation energy.
Unconstrained Equilibration - allows Mg++ to equilibrate in the protein without fixed boundary constraints, allowing us to judge the effects of these constraints.
Histograms - allows us to make
histograms of ion-oxygen distance.