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If I have one program run through a proxy then turn on my vpn, will the vpn "override" the proxy? The case is, I want all my traffic to be encrypted over the vpn but I want the speed of the proxy in this one program and still be encrypted by the vpn, is this possible? Can I run this one program through the proxy and still have the traffic encrypted through the vpn at the same time or will the program using the proxy be unencrypted?

Second question, any good program I can use to analyze my network traffic so I can test this myself?

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Based on my understanding, yes, the vpn setting will override the setting of proxy. Therefore you cannot use both proxy and VPN at the same time. The reason of the slower speed of VPN is due mainly due to the encryption between the VPN client and VPN server. So you simply cannot enjoy the speed of proxy while the data encrypted by VPN.

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