From: Mo Chen (mochen.mmm_at_gmail.com)
Date: Mon Jul 21 2014 - 15:23:06 CDT

Hi Aron,

Thank you very much for the prompt response! So the NAMD user guide was not
correct in saying that the unit of forceConstant is kcal/mol? I am
confused. Do you mean that the definition of forceConstant here is the K in
my equation, which is the usual definition in most of the MD simulation
packages? Thank you very much!

Best,
Mo

On Mon, Jul 21, 2014 at 1:12 PM, Aron Broom <broomsday_at_gmail.com> wrote:

> 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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