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.
Is this low output expected in this case? Why am I not getting more output structures when more computation time / trajectories are used? Any information or ideas on how to increase the output for the larger calculations is welcome!
-in:file:s input/my_protein.pdb -remodel:blueprint input/resfile -run:chain A -remodel:num_trajectory 32 -use_clusters false -nstruct 1 -ex1 -ex2 -packing:extrachi_cutoff 5 -use_input_sc -packing:linmem_ig 10 -no_optH false -find_neighbors -hb_srbb 1.0