From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Jul 21 2014 - 15:12:06 CDT
when you define a harmonic restraint, the restraint has its own center and
forceConstant. These things are individual to the restraint, as they go
inside its braces:
harmonic {
name myForceOne
center 1.0
forceConstant 1.0
}
harmonic {
name myForceTwo
center 2.0
forceConstant 0.5
}
or something like above (check the syntax in the manual), but the main
point being your colvars file can have as many restraints as you want. So
all forceConstants are unique to their bias and the units will match with
the centers. This is the same idea as the colvars themselves, you can have
as many as you wish and they all can have their own atoms or other
definitions.
In your equation, W is the work, or energy of the harmonic (the thing that
actually affects the MD), K is the forceConstant, r_ref is the center.
On Mon, Jul 21, 2014 at 4:03 PM, Mo Chen <mochen.mmm_at_gmail.com> wrote:
> Dear NAMD developers,
>
> Regarding the "forceConstant" (the scaled force constant) in harmonic
> restraints, as demonstrated in NAMD user guide. I have two questions:
>
> 1) Does this mean that if setting a 2D umbrella sampling, there is no way
> to individually define the force constants (with the unit of kcal/mol A^2
> or kcal/mol degree^2) for distance and angle? If there is a way to
> individually define them, how should that be done?
>
> 2) May I confirm with you about my understanding of the "forceConstanct"?
> According to the biased potential in case that the reaction coordinate is
> the distance, W = K/2*( r - r_ref)^2, here it basically says W is defined
> by "Forceconstants" and that K is dependent on W and r_ref?
>
> Thank you very much!
>
> forceConstant < (harmonic) Scaled force constant (kcal/mol) >
> Acceptable Values: positive decimal
> Default Value: 1.0
> Description: This defines a scaled force constant for the harmonic
> potential. To ensure
> consistency for multidimensional restraints, it is divided internally by
> the square of the specific
> width for each colvar involved (which is 1 by default), so that all
> colvars are effectively
> dimensionless and of commensurate size. For instance, setting a scaled
> force constant of
> 10 kcal/mol acting on two colvars, an angle with a width of 5 degrees and
> a distance with a
> width of 0.5 °A, will apply actual force constants of 0.4
> kcal/mol×degree−2 for the angle and
> 40 kcal/mol/°A2 for the distance.
>
> Best,
> Mo
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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