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

From: sunyeping (
Date: Tue Apr 05 2016 - 04:10:59 CDT

Dear Norman,     Maybe you are right, but I am not sure.     The conformation 1 I mentioned corresponds to the state that both termini of a short peptide bind to a protein of two long chains, and the conformation 2 corresponds to the state that one terminus of the short peptide dissociates with and strecthes away from the protein.     The transition from conformation 1 (the initial crystal structure) to conformation 2 can occur at a relatively smaller boost energy with the whole protein structure seeming to be normal. Increasing the boost energy leads to the distortion of the whole protein together with the transition from the conformation 1 to 2. It seems to me that the distortion or disorder is irrelevant to the transition, and it does not predict the transition paths, neither. So I can hardly believe that adding a larger boost energy can lead to the transition from the conformation 2 to 1. Instead, I tend to guess that a larger boost energy will lead to more serious distortion or even collapse of the protein (dissociation of the two long chains), or dissociation of the whole short peptide from the protein. I may presume that in a extremely entended aMD this collapse process could reverse, but I cannot afford such a long-time simulation. So it is important to design the simulation rationally. Best regards. Yeping

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