I need to run a series of Forcite MD runs to improve statistics and would like to automate the procedure by using Pipeline Pilot. To this end, I created a very simple protocol of which I have pasted an image in this note. The protocol takes a series of structures from a study table, runs the MD simulation successfully, but fails to save the output in a study table as I intended. What is the proper procedure to save the trajectories in either a study table or a series of xsd files?

Although an answer to the above question will solve my dilemma, I am also curious as to how to construct a pipeline that will run a given MD simulation for "n" times for a single given input structure while saving each of the trajectories and final structures in different folders. I find the documentation and examples of how to construct loops or even carry out simple tasks very weak. Looking at more sophisticated examples when you don't understand the basics is not an efficient way to learn how to use Pipeline Pilot.