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A) The first thing to check if your code is slow is if it’s a release-mode compile. It should say release and NOT say debug in the executeable file name. (I don’t recall us suggesting you tweak compiling, so I doubt this is the problem).
I believe we got to a point where you have a centroid version of your heme, and are doing standard docking with the centroid heme in place (followed by fullatom docking with the fullatom heme in place; all as part of one trajectory). Is this correct? Is your slowdown in the fullatom or centroid phase? I think you can tease out where the code is by what it is outputting. Briefly, DockingLowRes is the centroid phase, and DockingHighRes is the fullatom phase. If you see core.pack.task, that’s high-res. We can try injecting some timing statements into the code to see where the slowdown is.
You may want to go ahead and post your exact command line for later reference.