This is from someone who knows more than I about the broker (Chris Miles):
“I don’t believe the broker can handle multiple configuration files. The behavior that the user describes is curious though– I would have expected the last configuration file mentioned on the command line to overwrite all previous ones. If I understood him correctly, he observed the opposite behavior.
The most obvious suggestion is to combine broker configuration information into a single file. I suspect that he separated some of the configuration options into multiple files to try out different scenarios. I routinely do this for trajectories beginning from a template. There’s a certain set of “base” flags that never change, as well as template-specific information (e.g. template pdb, alignment, constraints).”