Ensemble

An ensemble defines a molecular system and all the conditions that remain fixed for its entirety:

• Force field parameters;
• Simulation temperature;
• Molecular topology;
• Environmental assumptions (e.g., solvent, pH);
• Scoring functions for docking, etc.

These are defined by fields that use cadence: ensemble, and are meant to remain constant within that ensemble.

A new ensemble must be created if any of these assumptions change. For example:

• A molecular dynamics simulation run at pH 7 is one ensemble.
• The same system at pH 5 is a different ensemble.