From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Aug 23 2016 - 20:02:37 CDT
I used the eigenvector colvar for a simple transition between two close states of a protein (RMSD = ~2.6 A). One curious thing I observed is that the minimum falls at 0.5; in fact, I saw this in other runs as well, even using different starting structures. For something like RMSD, it seems obvious that there will be more conformations accessible the more you increase RMSD, which would lower the energy. I can’t convince myself if that is the case here, however. Certainly, it seems that each value of the colvar (in my case normalized from 0->1) does not dictate a unique structure, but is there a clear relationship with where one is on the path and the number of accessible states? In which case, only the end points can truly be trusted?
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