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First regarding rake for lower stakes, e.g. NL50 I used 5% rake and 60chip cap with 1000 chips. Is this correct to use because you can`t have 0.5 chips as SB or BB.
Yes, 60 chip cap is 6bb in 5/10 and in 50NL 3$ is 6bb as well (0.5$ * 6) so that's the correct way.
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And when I run a preflop sim and then save the small/very small tree i can`t use them for nodelocking etc later on?
Yes, as small saves don't have all river solutions (just cached EVs for flop/turn) any change in strategy would mean that EVs can no longer be shown. That means that things like rounding or node-locking won't work.
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But I will still be able to browse the strategy, EV and ranges right?
Yes, the solver recalculates missing parts of the tree automatically. If you have turns saved then the process is usually very fast (200ms more or less is expected) but if those are very small saves then ra-calculating turns may induce significant delay.
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What would you recommend when someone wants to be able to use the runned simulations agai
If you want to browse it - small saves are good.
If you want to node lock then you need to build the tree again, node lock, solve. It's not a problem though as node-locking on already saved tree wouldn't be faster than on a fresh one and sometimes the solver have big problems coming back from precise solution once you mess up with it by node-locking. I recommend nodelocking on fresh trees or on ones solved for just a little time.
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Basicly I am not sure, weither or not to download the big trees from my dedicated server.
I honestly can't see one reason to download full tree saves. Remember that to load a full tree save you need as much RAM as the original tree took (so 32-64GB in your case) while to load a small save you need barely any RAM.