A customized protocol merges multiple CHARMm trajectory files followed by trajectory analysis (rmsd, torsion, distance…). Attached please find the custom DS protocol (Merge & Analyze Trajectory.xml) with an example (including all input/output files).

*How to import DS protocol:
(1) Download the attachment (protocol).
(2) Open Discovery Studio 2.1 client
(3) In the protocol explorer panel, right click at your folder to import the protocol
(4) Double click on the protocol to open its parameter explorer.

*How to setup the job:
>Input Molecule: load molecule (single conformation) into DS
>Input Trajectory: specify multiple dcd files (the user can copy/paste the path and file names in an order, which are separated by ",").

Thanks to Eric Yan and Tina Yeh for merge_trajectory script and component.