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fhh2626 / BFEE2

binding free energy estimator 2
GNU General Public License v3.0
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forceconstant values for free energy calculations #93

Closed ndonyapour closed 1 year ago

ndonyapour commented 1 year ago

Hello,

I'm running simulations using your method (BFEE2) and I have a question about the forceconstant value in the free energy calculation function (e.g. geometricRestraintContribution). Is this the force constant defined for each harmonic restraint or is it the scaled value of it (forceconstant is scaled according to the specified width)?

Thank you!

fhh2626 commented 1 year ago

Hi ndonyapour,

In BFEE2, whenever a harmonic block is defined, the width is not specified for the corresponding CV, which imply that the forceConstant is exactly k.

Haohao

ndonyapour commented 1 year ago

Thank you for the response! I thought you use the force constant from harmonicWalls.

fhh2626 commented 1 year ago

That's another story. The force constant from harmonicWalls guatantees sampling within the current window and should not affect the result. You can also use an reflecting boundary whenever you want.

ndonyapour commented 1 year ago

That explains why. Thank you for your quick response!