I need to know whether the exact initial position of ion within each window to calculate the free energy via the ABF method is important, and what would be the best position for this purpose? Thanks.
I don't think the exact position is important. Any meaningful position would be fine: I guess you need to equilibrate each of the windows, so the position would change anyway.
Your question is however a bit too general. If you want to study a reaction which is highly affected by the local ionic environment, then the attention you pay should be definitely higher...
Thank you so much for your answer. Actually, I want to calculate the PMF profile along the reaction coordinate using colvars in NAMD. I did SMD simulations (with a constant velocity of 10 A/ns) to pull the ion along the permeation pathway and want to use its different snapshots within each window, so I wanted to know which snapshots are better to choose from, in the middle of the window or close to the constraint walls?
Do you think that I still should equilibrate each of the windows even if I have used these snapshots from SMD simulations?
You may have a look to this question I asked.
https://www.researchgate.net/post/Why_do_we_divide_the_region_of_interest_in_different_windows_in_ABF_in_NAMD
https://www.researchgate.net/post/Why_do_we_divide_the_region_of_interest_in_different_windows_in_ABF_in_NAMD
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