Need some help with pcsx2 performance
pcsx2 has run like a dream since i bought a new computer but after replacing the GPU (GTX 950 to a GTX 1060) i have seen that my games performance has dropped, i was able to comfortably play through games like r&c 3 and MGS3 at 60 fps with 0 Drops. but now the game runs slowly throughout any help would be appreciated

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Check your Nvidia control panel. Manage 3d settings-program settings-and select pcsx2.exe (add it if not in the list already). Under this make sure that the preferred GPU is your Nvidia card and that under OpenGL rendering GPU it is also the Nvidia GPU. It also does not hurt to make sure the power settings is set to prefer maximum performance either since it is not a laptop.

For some reason most GPUs do not see emulators as workloads that need to be run on the dedicated hardware and dumps it off on to the slower integrated GPU (unless you are running one of the rare no iGPU Intel chips or a Ryzen CPU not APU). And yes, generally if you replace your GPU or uninstall and reinstall your control panel then you may have to redo these settings for this emulator (a few other emulators too) and some games that do not register as a workload that the GPU needs to work in (the dot hack GU PC game is one of these for some reason, and enter the gungeon)

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