runZero can be used to scan VMware virtual machines. However, there are some precautions you should take.
VMnet interfaces normally use Network Address Translation (NAT) to route traffic between the host system and the virtual machines. The VMware software effectively operates as a stateful router. As explained above, this can cause problems when runZero tries to open thousands of connections.
For scanning VMware systems, the best option is to deploy a runZero Explorer inside VMware, on a virtual machine connected to the VMnet you want to scan. That Explorer should be able to scan all VMs on the same VMnet without VMware needing to track all of the connections.
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