Hi all, I am reading the paper "Replica-exchange molecular dynamics method for protein folding" by Yuko Okamoto. In this paper, they exchange temperatures of 2 replica. To evaluate that replica exchange is successful, they calculate exchange probability; plot the temperature, potential energy per replica versue time. In Gromacs, coordinates of replica are exchanged instead. So besides evaluating exchange probability, how do I know that the replica exchange is sucessful? Since we exchange coordinate, one replica just stay at 1 temperature, so we will not see the result of the paper by Yuko, I mean, one replica actually visit all the temperature. How about potential energy, should I expect that one replica visit all range of potential energy when we exchange coordinates of replica? Also, is this bad if exchange probability too high, let's say 0.8? Thanks in advance. Best regards, *Lan Hoa* -- Gromacs Users mailing list
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