[gmx-users] Bonds definition in itp files

[Sina Omrani]

Thanks, dear Justin. if I define a constraint on a bond then force constant
isn't useless?

On Mon, 6 Apr 2020 at 17:12, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/6/20 7:24 AM, Sina Omrani wrote:
> > Hi,
> > I wanted to know how we specify a bond order in our simulation? For
> > example, if we have a triple bond in our structure between atoms 1 and 2,
> > is it by length and force constants or we define 1 and 2 bonds three
> times
> > in the bond section of itp file?
> > What if we use a constraint on this bond? because I get better results
> when
> > I define the bond three times but haven't seen this method. is it wrong?
>
> All interactions should be defined only once, and the parameters used
> should produce correct behavior. MM force fields have no concept of
> double or triple bonds; they only know the stiffness of the spring
> connecting the atoms. My guess is that if you had to add the bond three
> times, the force field parameters are adding together, indicating that
> the force constant is unsuitable for what you're trying to and needs to
> be refined.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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