Understand the "Reweighting the results" in the "Belfast tutorial: Umbrella sampling"

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Zhang Cheng

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Nov 5, 2018, 5:22:49 PM11/5/18
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Dear All,
In the Section "Reweighting the results" of Tutorial "Belfast tutorial: Umbrella sampling"

I generated two COLVAR plots (raw COLVAR files attached)
1) KAPPA=10.0 AT=-2 (left)
2) KAPPA=0.0 AT=-2 (right)

Can I confirm my understanding?

1) The "AT" argument defines the position of the restraint. That is reason that the phi values fluctuates along the -2 in the left plot. 

For the right plot where KAPPA=0, the AT should not affect the restraint because k/2*(x-x0)^2 always equals to 0. But why the phi values also are around -2 ?

2) Is the unit of phi (purple dots) degree (i.e. °) ? So it could be from -360° to 360° ?

Is the unit of "restraint-phi.bias" (green dots) kJ/mol ?

In this tutorial, it is said 
The keyword KAPPA determines the hardness of the spring constant and its units are [Energy units]/[Units of the CV].
However, I think its units should be [Energy units]/([Units of the CV]^2), so in this case, should it be kJ/(mol*degree^2)?

3)  In the equation k/2*(x-x0)^2, k (i.e. KAPPA) and x0 (i.e. AT) are defined. Is the remaining variable "x" a random value at different time points? Why in the left plot, most green dots are within the range of 0 to 5 ?


2018115-212143.jpg2018115-212257.jpg



4) I also plot the psi only for the KAPPA=10 (left) and KAPPA=0 (right) as shown below. They are not exactly the same, but because they look similar, this indicates that the restraint on phi does not affect the psi values. 


2018115-221140.jpg2018115-221737.jpg




Thank you very much!


Yours sincerely

Cheng 


 

COLVAR0
COLVAR10
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