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markovModel(lag,n + 1) #55
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Getting n-1 is normal. Has to do with the implementation of PCCA. The real problem here seems to me that your data is extremely disconnected and at a lag of 50 frames you are throwing away 75% of your data, having only essentially 16 trajectories of data left. |
p.s. there is a new option |
Thanks, I like the It just happened in another system where I actually have a lot of data and |
Well, it depends how you interpret it. I would not trust kinetics of the macrostate with has only occurred in 2 trajectories. Bootstrapping for example would give you huge errors. The way I usually think about it is:
The more macrostates you add the more macrostates you will get with bad statistics. Also look at your timescales. If you only have one slow process, the correct thing to do would be to make 2 macrostates for example. Thinking about it, I would love to have a feature like ace = AcemdLocal()
ace.submit(model, macro=2) which starts simulations from macrostate 2 to improve sampling! |
ok, thanks! |
Hello!
Question. It seems that sometimes lately when I try to build n macrostates I get n-1, is this an error?
Thanks,
Noelia
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