Re: AW: why does the transition seem to be irreversible in aMD

From: sunyeping (sunyeping_at_aliyun.com)
Date: Tue Apr 05 2016 - 02:47:39 CDT

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Dear Norman, 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. Best regards. Yeping

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