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Posted By: vidhya Umbrella sampling reaction co-ordinate - 12/06/19 06:59 AM
Hey all,

I am using umbrella sampling technique to constraint the distance between two segments of protein defined by the reaction co-ordinate.
As per the theory, the distance constraint with a proper force constant should ideally sample around the given distance.
For example, let's say, for 9 A distance constraint, the segments can interact between 8 and 10 A, (9 + 1) However, for me, it samples between 10 and 11.
Sampling of (9 + 1) happens with a distance constraint of 8 A.

If there is a barrier at these distances, a distance constraint of 8 A should not sample around 9. Why is the shift happening. I have tried using higher force constants. But it doesnt work.
Can somebody explain why this happens?

I have attached the histogram to explain my problem better. Please advise.

Attached File
histogram.png  (59 downloads)
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