The Measure Trajectory Features protocol is useful for measuring  molecular dynamics time-series features such as root-mean-square distance from a reference conformation (RMSD), solvent-accessible surface area (SASA), dihedral angles (Dihedral), and intermolecular or intramolecular distances between nearest atoms of residues (Distance). 

The required parameters are an Input Molecule (i.e. a .dsv file loaded into the DS Client) and and Input Trajectory (a corresponding .dcd file containing the frames of the trajectory).

The Input Molecule does not need to contain conformation since these are loaded from the dcd file. However, the molecule and corresponding trajectory must be for a simulation run with explicit solvent. The first step this protocol performs is to remove the solvent in order to perform the calculations. 

One of the benefits of this protocol is that it does not require the user to load a large trajectory into the interface in order to perform these calculations. Another benefit is that the user can specify multiple .dcd files in one job.