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Laplacian bond order this method is an extension of the qtaim (quantum theory of atoms in molecules) concept of using the laplacian of the electron density $\nabla^2\rho$ to characterize bonding When a.cif file is opened in vesta, there are some default values of min and max bond lengths between two atomic speci. Standard qtaim just uses the value of $\nabla^2\rho$ at bond critical points (minimum electron density along the bond, max along orthogonal directions), but these values are unintuitive and often don.

If you are using gaussian to run your calculations, just output the calculated wave functions and use the multiwfn to run the topology analysis. I need some cutoff radii to count bonds between different atoms in my system Can i estimate the bond energy by running a single gaussian calculation of the fragments at very long separation (say, 40 angstroms)

Or do i have to calculate each fragment without the other?

2 i'm working on a diatomic molecule and need to accurately describe its bond dissociation energy I plan to perform bsse correction (counterpoise or some other) for this molecule While gaussian handles this in a single step, i'm struggling with how to carry out this correction in orca. I'm studying hydrogen bonds in a water system

The commonly accepted parameters are To analyze the hydrogen bonds, i plotted the number of hydrogen bond. In the image you posted in the question, the bond between 5 and 6 is long, so during the scan, the bond length would have to decrease which is why the step size is negative. A bond is present when the distance between two atoms is lower than the sum of the van der waals radii of the two atoms

Van der waals radii are typically looked up from a preexisting table, not calculated

We can find such tables in chemical reference books or online For instance, here is a link that supplies the following van der waals radii. I have some results about the energy of h2 as a function of the bond length using restricted hf (rhf) and unrestricted hf (uhf) methods Hi @magic_number, after running with more recorded timestep, i think the main reason is because the molecule pass through zlo and have atom deleted, as result, the bond connecting that atom is lost

But i know having a fixed z boundary is possible to run because that's what i found from several lammps papers.

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