Problem with running large simulation files

Hello,
I want to run a 2ns simulated output structure for further dynamics production steps. Everytime I try to run the protocol it shows a server error (either cannot connect to server or that the components installed on the current version of the pipeline pilot are not compatible with the client's version). I am able to run the same protocol on the previous output structures, for example the output generated after 1ns. But after 2ns nothing seems to work, no other protocols either.
Could it possibly be a problem with the structure file? or are there some limitations on large output files in DS that I am not aware of?