Standard qtaim just uses the value of ∇2ρ ∇ 2 ρ at bond critical points (minimum electron density along the bond, max along orthogonal directions), but these values are unintuitive and often. When you are scanning two bond lengths in gaussian, you step once through the first bond scan, and complete stepping through the second bond scan 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. 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
When a.cif file is opened in vesta, there are some default values of min and max bond lengths between two atomic speci. 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. I want to add a bond between specific atoms I found on vmd page that one can use topotools (e.g Topo addbond 1 2 ), but i have a lot of residues so this method didn't work with me Can i estimate the bond energy by running a single gaussian calculation of the fragments at very long separation (say, 40 angstroms)
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.
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