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To backup entire virtual machine while are running, you have to use the VBC provided by vmware.
this is a commandline tool that speaks with your VirtualCenter and tell it to create a Snapshot of a virtual machine, then detach it and copy the vmdk files to a location.

Take a look here http://www.vmware.com/products/vi/consolidated_backup.html to understand how it work.

the sintax of the command is like this:

vcbmounter.exe -m nbd -h yourvitualcenter.yourdomain -u username -p password -a name:VMname -t fullvm -r pathwheretosave

With "-m nbd" you can backup your Vm through an ethernet instead of a FibreChannel SAN connection.