# Bond parameters **URL:** \ **Category:** User discussions\ **Created:** [April 27, 2024, 8:10pm UTC](https://gromacs.bioexcel.eu/t/bond-parameters/9006 "2024-04-27T20:10:22Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![ahosseini9473](https://avatars.discourse-cdn.com/v4/letter/a/e274bd/32.png) [@ahosseini9473](https://gromacs.bioexcel.eu/u/ahosseini9473)\ **Post date:** [April 27, 2024, 8:10pm UTC](https://gromacs.bioexcel.eu/t/bond-parameters/9006/1 "2024-04-27T20:10:22Z")
Hi, I am trying to simulate a material in Gromacs. however, I am using parameters used in lammps. There is a confusing part which is related to the bonds. based on what I read from the article, the bond between Ti and O is at the length of 2.1 A (0.21 nm) and the force constant is 400 Kcal/mol (1673.6 kj/mol). Now the question I have is that what type of bond it is. I searched here as well but so far haven’t been successful to understand it. I would be very appreciative if someone could help me understand this. ---
**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Post date:** [April 29, 2024, 3:46pm UTC](https://gromacs.bioexcel.eu/t/bond-parameters/9006/2 "2024-04-29T15:46:03Z")
To me, it looks like a [standard type-1 harmonic bond](https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#id36), emulating a fixed covalent bond between two atoms. Note that the unit of a force constant is not the unit of energy, but the unit of force per distance, or energy per distance², so you need to factor in the distance unit conversion factor (1nm/1A = 10) squared (=100). ---
**Author:** ![ahosseini9473](https://avatars.discourse-cdn.com/v4/letter/a/e274bd/32.png) [@ahosseini9473](https://gromacs.bioexcel.eu/u/ahosseini9473)\ **Post date:** [April 29, 2024, 9:38pm UTC](https://gromacs.bioexcel.eu/t/bond-parameters/9006/3 "2024-04-29T21:38:37Z")
I was reading this, [https://www.ks.uiuc.edu/Research/vmd/current/ug/node237.html](https://www.ks.uiuc.edu/Research/vmd/current/ug/node237.html), last night. it looks like the force constant reported is scaled one. Meaning if the length of the bond is 2.1 A then the spring constant used is 400/(2.1^2) kcal/mol/A^2. ---
**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Post date:** [April 29, 2024, 10:10pm UTC](https://gromacs.bioexcel.eu/t/bond-parameters/9006/4 "2024-04-29T22:10:13Z")
But this is the documentation of the Colvars module, which is used for defining and biasing collective variables. The scaling coefficient is equal to 1 by default, and is only useful for multidimensional restraints with a unique force constant. If you’re transferring parameters from LAMMPS, you might want to check their definition of the harmonic bond, in particular whether they put the ½ factor in front if the k(x0-x)² - for example, AFAIK Gromacs and NAMD do but Amber doesn’t. Otherwise it’s usually just keeping track of units. ---
**Author:** ![ahosseini9473](https://avatars.discourse-cdn.com/v4/letter/a/e274bd/32.png) [@ahosseini9473](https://gromacs.bioexcel.eu/u/ahosseini9473)\ **Post date:** [April 29, 2024, 11:52pm UTC](https://gromacs.bioexcel.eu/t/bond-parameters/9006/5 "2024-04-29T23:52:27Z")
Thanks, so you mean, I just have to divide 400 kcal/mol to 1 A^2 so that K = 400 kcal/mol/A^2. In case of lammps, regarding the documentation, [bond\_style harmonic command — LAMMPS documentation](https://docs.lammps.org/bond_harmonic.html), 1/2 is included in the K. So that k = 2 \* 400 kcal/mol/A^2. ---
**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Post date:** [April 30, 2024, 10:45am UTC](https://gromacs.bioexcel.eu/t/bond-parameters/9006/6 "2024-04-30T10:45:34Z")
> [@ahosseini9473](#): > > so you mean, I just have to divide 400 kcal/mol to 1 A^2 so that K = 400 kcal/mol/A^2. There’s no need to divide anything in principle, this is a formula not related to bonded terms but arbitrary harmonic restraints. But still, that would not change anything. > [@ahosseini9473](#): > > 1/2 is included in the K. So that k = 2 \* 400 kcal/mol/A^2. So yes, seems you need to do 2 \* 400 \* 4.184 \* 100 to get the force constant in Gromacs units. It’s also good to double-check that with an example parameter set that was officially published for both Gromacs and LAMMPS. ---
**Author:** ![giacomo.fiorin](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/giacomo.fiorin/32/2862_2.png) [@giacomo.fiorin](https://gromacs.bioexcel.eu/u/giacomo.fiorin)\ **Post date:** [April 30, 2024, 5:31pm UTC](https://gromacs.bioexcel.eu/t/bond-parameters/9006/7 "2024-04-30T17:31:12Z")
@ahosseini9473 For context, the Colvars definition of a harmonic potential includes the scaling parameter `width` because it is defined on collective variables of very different kinds, which may have very different units. In a force field, the harmonic potential is always defined on a distance, and so the unit is always known: no need to scale anything there. BTW the VMD doc page you linked is really old (VMD 1.9.3 is 8 years old). For other forum readers, I’m linking [here](https://colvars.github.io/master/colvars-refman-gromacs.html#sec:colvarbias_harmonic) the relevant Colvars doc page for GROMACS. Giacomo