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which pcsx2 version are you using. latest appimage from site ?

Optimizing PCSX2 for MGS2 can be a tricky task, but there are some things you can try to improve game performance. First, make sure you have the latest version of PCSX2 installed, as newer versions often include performance improvements. Additionally, try adjusting the emulator settings, such as the EE/IOP and VU cycle rates, as well as the graphics settings like the internal resolution and texture filtering.