Good evening, I would like to ask for your help because I am trying to run the pepspec anchor dock protocol, so I am using the following options as flags, which come in the tutorial:
I am trying to design a helical linker between two strongly interacting subunits that connects their termini using RosettaRemodel.
I am running remodel with the following flags in mpi mode and get the desired output (around 2-4 structures with -num_trajectory 32). However when I increase -num_trajectory to e.g. 1000 I still get only around 2-4 strucures out (named 1.pdb 2.pdb ...). while computation time increases drastically.