From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Apr 05 2016 - 03:06:43 CDT
Usually that’s how conformational sampling is about to work. The structures that you call disordered or distorted are part of the conformational space and also part of the transition paths between intermediate local minima. You will have to sample some amount of data and analyze the probability of states e.g. by creating histograms of proper reaction coordinates like rgyr and mainchain hbonds and compute free energies from it. This will also tell you the amount of energy required to do the transition you mentioned.
Von: sunyeping [mailto:sunyeping_at_aliyun.com]
Gesendet: Dienstag, 5. April 2016 09:48
An: namd-l <namd-l_at_ks.uiuc.edu>; Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: AW: namd-l: why does the transition seem to be irreversible in aMD
Thank you for your replay. You are right that the aMD is aimed at conformational sampling but I wish to see that transitions between the two conformation occur alternately. It seems that the transition from conformation 1 to conformation 2 is easy in my aMD, but not vice versa. However, if I keep increasing the boost energy, the whole protein structure becomes distorted and many structural motifs become disordered in addition to the conformational transition I am studying. So I guess simply increase the boost energy may be not a wise strategy.
From:Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >
Time:2016 Apr 5 (Tue) 15:30
To:namd-l < <mailto:namd-l_at_ks.uiuc.edu> namd-l_at_ks.uiuc.edu>, 孙业平 < <mailto:sunyeping_at_aliyun.com> sunyeping_at_aliyun.com>
Subject:AW: namd-l: why does the transition seem to be irreversible in aMD
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> [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von sunyeping
Gesendet: Dienstag, 5. April 2016 05:21
An: namd-l < <mailto:namd-l_at_ks.uiuc.edu> 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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