Is transition time(mfpt) from one state to another may be different from time observed in MD simulations?

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Is transition time(mfpt) from one state to another may be different from time observed in MD simulations? #1542

Closed Bazzinga18 closed 2 years ago

Bazzinga18 commented 2 years ago

Hii, For a particular protein it takes few microseconds to unfold its helix through the MD simulations but through MSM, mfpt for the folded state to the unfolded one is quite different. what was the reason for this??

thempel commented 2 years ago

Can you specify, what is "quite different"? In case the MFPT is extremely high compared to your observation, maybe the MSM is not connected - you may want to double-check that you have properly sampled both the folding and the unfolding.

Bazzinga18 commented 2 years ago

from simulation the time for unfolding comes out to be around 6-8 microseconds and from msm it comes out to be in the range of 100 microseconds

stale[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

clonker commented 2 years ago

I assume this has resolved itself and/or is no longer relevant, otherwise feel free to reopen. I concur with @thempel that this sounds like not connected MSMs or not enough data (as in, e.g., you observe only one direction of the process)