Conformational sampling is a process of collecting conformers. Conformer is a particular arrangement of a system in harmony with its character.

Conformational sampling is a process of collecting conformers. Conformer is a particular arrangement of a system in harmony with its character.

It might be that the conformer term needs to be clarified. It denotes a specific arrangement of atoms in real space (atomic nuclei) such that forces acting on atoms (nuclei) are totally compensated by each other. Without accounting for always presented atomic vibrations one conformer correspond to one saddle point on potential energy surface (where the first derivative - integral force - is equal to zero). Sampling in moldynamics is merely a search of these saddle points using treatment of equations of atomic motion.

Studying directly of long md trajectory frames are difficult and even confusing, so using some methods like principle component analysis (PCA) or other methods dealing with trajectory can be helpful. These methods based on their strategies classify trj. to different clusters.

If you are doing molecular dynamics, you would like your trajectories to include all possible conformations of your system in order to properly estimate your desired properties. Depending on your approach, your trajectory could get stuck in a local minima, resulting in bad conformational sampling. This is analogous to doing a poll and not asking for everyone's opinion, you won't get answers that reflect what everyone is thinking.