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For a list in my site, i need to set custom permissions based on the user loggin in. To set this, i select "List permissions" from the list tools ribbon, then i select "Stop inheriting permissions". This should allow me to create custom permission for the list, but when i add some user to the groups (members, visitors or owners), the changes i do here also affects the rest of the site, and vice versa what i modifiy outside this list permissions reflects on it.
Am i doing something wrong?
No, you are doing nothing wrong.
The groups you created are site wide groups, they are not limited to one Sharepoint list. So when you add a user to any group and this group has permission "Read" for your list, this user will receive read permission for your list. The user will also be added to the general group, so if this group has site-wide read access your user will have site wide read access.
MySiteCollection has following Groups: "Special Reader", "Special Admins".
MyList has unique permissions, not inheriting from MySiteCollection
So basically when you click "stop inhering permissions" you can set special permissions for existing groups/users, you do not create new groups.
PS: However you could of course another group, only including users for MyList with special permissions for MyList and no permissions for MySiteCollection.
The behavior you are experiencing is “by design”. When you stop inheriting permissions from parent, SharePoint copies the groups/users and permission levels assigned to the group/users to your list. Now read your permissions to the list this way: “Members have ‘contribute’ permission level to the list” Or “All users belong to members group have Contribute permission to the list and membership to this group is managed at site collection level not specifically for your list even if you stopped inheriting”. If you change membership of that group it affects everywhere that group is used. If you want a different behavior, you have several choices depending upon the governance practices at your side. For example, you can assign “read” permission to members group in your list. If you do so, all users belonging to that group will have Contribute permissions through your site but only read permissions to your list.
There is a nice while paper for best practices about manage fine grained permissions: http://download.microsoft.com/download/C/1/D/C1D02A30-B2EC-4B7D-A267-B983085F1A91/sharepointfgpbestpractices.docx
