From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jul 22 2014 - 04:37:30 CDT
That's correct. You actually have two choices:
- you want to couple the two variables in a single 2D bias, for instance
because you want to make that a time-dependent bias, and it's simpler to
define it just once. In this case you set the relative force constants by
explicitly setting the width of each variable.
- or you can define two independent harmonic biases, as in the example
given by Aron above. Then you will probably keep the default width at 1,
and the force constant will have its natural unit of kcal/mol/U^2, where U
is the colvar unit (most of the time, Angstrom or degree).
Best,
Jerome
On 21 July 2014 23:57, Mo Chen <mochen.mmm_at_gmail.com> wrote:
> 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