Hi,
I am performing MD of a protein with two conformational states.
Structures of both these states are available in RCSB PDB. The protein is
small and simulates at a rate of ~500 ns/day (~15 microseconds/month) at
2fs timestep.
I have independently simulated the two conformations to 25 microseconds
each but failed to see transition between them. I also tried adaptive
sampling and can observe that both conformations can possibly transition
into one other. There seems to be a high energy barrier that conventional
MD is unable to pass through. I want to observe the transition between
these two conformational states and estimate the rate of transition.
I have been informed by my experimental collaborators that the
transition rate might be in hundreds of microseconds but lower than
millisecond. What method implemented in AMBER can be used to estimate the
rate of transition in this case.
Regards
Abhilash
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Received on Mon Jul 22 2024 - 09:30:02 PDT
