From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Sun Feb 13 2011 - 15:08:26 CST
Dear NAMD experts,
This may seem simple, but I have tried to run ABF simulations with exactly the same input files to test the reproducibility of the results. I know that after overcoming the energy barrier, the ion moves under its diffusion (ion channel dynamics) and I expect to get the same results using the same input files. But, the sampling profile and also the force behavior I get, are not the same (sampling at one side of the window is 25K while for the other simulation it is 250k). Do we expect to get exactly the same profiles (especially the same SAMPLING profile)? If not, what determines this? Is there any random factor involved?
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