Dear Amber users,
I am studying the loop dynamics of a large protein. I defined a 1D reaction coordinate and already obtained a nearly converged free energy curve using ABMD. But this free energy curve is not that smooth, further refinement is required. However, due to its large size, computational expense will be very demanding. So, I am thinking that maybe I can use umbrella sampling to further refine this curve. My question is that whether these is any rule to choose the biasing potential at any reaction coordinates based on the coarse free energy curve.
Please feel free to correct me if my idea is not correct. Any comments or suggestions are appreciated.
best wishes,
Ye
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Received on Mon Mar 14 2011 - 21:30:03 PDT
