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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 Topo addbond 1 2 ), but i have a lot of residues so this method didn't work with me 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.
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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 I found on vmd page that one can use topotools (e.g 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.
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. 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?
No, classical molecular dynamics cannot break bonds The potential you showed is the most common form of bond, the harmonic potential a.k.a If you have ever broken a bond in qm (calculated a dissociation curve), you know it is a bit tricky, you need to use unrestricted settings, meaning, that a given pair of electrons does not need share the same orbital If you are using gaussian to run your calculations, just output the calculated wave functions and use the multiwfn to run the topology analysis.
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
