First of all you have to shutdown VirtualBox machine that you wan’t to clone.
After that create new folder where you wan’t to clone existing vmdk machine to vdi
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$ mkdir new_vm |
After that run this command in terminal:
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$ VBoxManage clonehd --format VDI old_vm_machine.vmdk new_wm/new_vm_machine.vdi |
Wait until the job is done and… that’s all.