From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Apr 04 2016 - 22:21:00 CDT
Dear NAMD users,
I ran an aMD with NAMD and observed a transition in my structure from conformation 1 to conformation 2 within 10 ns. However, when extending the simulation, I couldn't observe the reversion from conformation 2 to conformation 1. Since the aMD is done by adding an extra boost energy to the simulation system, does that mean that conformation 2 is located in the high energy contour in the potential surface? Is the aMD biased to sample the conformations in the high energy contour in the potential surface rather than those in low energy basins? What can be done to biasly sample conformations in low energy basins? To be specific, how could I realize the reversion from conformation 2 to conformation 1?
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