Our lab is relatively new at docking and have never used scons before. We are trying to run docking simulations on a HPC using Snugdock, but are having trouble speeding up the process. The way that we are currently running the simulations, it is taking ~30 minutes to complete 1 model. I compiled the programs using the command './scons.py -j 10 mode=release bin extras=cxx11thread', but it seems that it is still unable to run on 10 cpus. The flags that we used were '-nstruct 10 -partners LH_A -spin -multithreading:total_threads 10'. I was wondering if you someone could clarify if there was a step that I may have been missing. Thank you.