I want to verify the effects of clock skew on a distributed system and the simplest way for me to do that is using multiple docker containers linked together.
Can I modify the clocks from individual docker containers so that they are decoupled from the host machine?
If you want to run a container with a different time, you can launch it with a different timezone, see this extract from https://github.com/docker/docker/issues/3359#issuecomment-32150214
I'm not sure that linked answer is entirely appropriate.
The simple fact is that containers are just processes: you can't do anything inside a container that you can't do in a normal subprocess. You can muck about with timezones and such, but they are still referencing the same kernel clock as anything else.
If you really want to play with time skew, you will probably need to investigate some sort of virtualization solution.