[gmx-users] Bonds definition in itp files

[Justin Lemkul]

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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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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