From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Apr 05 2016 - 02:29:42 CDT
Well If I’m correct, you don’t actually want your structure to get stucked in an aMD, as the main goal is to perfrom conformational sampling. So your boost potential might be too small to leave the rather stable structure your system ran into.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von sunyeping
Gesendet: Dienstag, 5. April 2016 05:21
An: namd-l <namd-l_at_ks.uiuc.edu>
Betreff: namd-l: why does the transition seem to be irreversible in aMD
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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