From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Fri Dec 03 2010 - 09:16:07 CST
Dear NAMD users
I need to get the PMF profile of a channel ion along the channel with RC=-20 to +20.In using ABF (adaptive biasing force) method, we believe that:
"Eventually, as the underlying free energy surface is canceled by the adaptive bias, evolution of the system along the reaction coordinate is governed mainly by diffusion."
To me that means it doesn't matter where I put the first position of my channel ion at the beginning as long as it is between -20 and +20. I mean even if I don't put it in the middle, it should have the chance to go through all the reaction pathway finally with almost the same number of sampling everywhere.
The reason I am asking this is that the ion has been spending much time in half of the RC and never has been in the other half so far. Just want to confirm that the begging position of the ion really doesn't matter as long as it is in the RC. Is that true?
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