From: Mo Chen (mochen.mmm_at_gmail.com)
Date: Mon Jul 21 2014 - 16:57:15 CDT
Hi Aron,
No problem for my previous question. I think I understand the forceConstant
now - it is the defined value (in kcal/mol) divided by the specific width
(default 1).
Best,
Mo
On Mon, Jul 21, 2014 at 1:23 PM, Mo Chen <mochen.mmm_at_gmail.com> wrote:
> 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
>>
>
>
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:37 CST