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Checkpointing interesting points in simulations and rerunning with modified parameters happens literally all the time

Especially weather / climate / geology and medicine

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They’re re-run, though. You don’t change the parameters in the middle of the simulation. That goes against the point of simulating something.

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You don’t rerun everything from scratch. Especially weather simulations can be checkpointed at places you have high certainty, and keep running forks after that point with different parameters. This is extremely common with for example trying to predict wind patterns during forest fires, you simulate multiple branches of possible developments in wind direction, humidity, temperature, etc. If the parameters you test don’t cover every scenario that is plausible you might sometimes engineer it into the simulation just to see the worst case scenario, for example.

And in medicine, especially computational biochemistry you modify damn near everything

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You’re confusing simulations of specific events with a simulation environment. If our universe is simulated, then it’s unlikely that the creators of the simulation would be interested in the individual occurrences you’re describing. The universe is what’s being studied, not the happenings inside of it.

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