What are the types of bond orders? - Matter Modeling Stack …
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 …
How may I calculate the bond length between two atoms?
Apr 26, 2021 · Bond formation could be something like 1-P $_ {break}$. You could also run quantum calculations for all possible pairs (or higher order clusters) of atoms or hit the …
Lost atoms in LAMMPS - Matter Modeling Stack Exchange
Nov 1, 2022 · 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 …
Scanning two bond lengths G-16 - Matter Modeling Stack Exchange
May 9, 2023 · 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. For example, consider …
How to choose sigma and epsilon value for carbon to calculate …
May 12, 2022 · How to choose sigma and epsilon value for carbon to calculate the bond coeff (lj units) in LAMMPS? Ask Question Asked 3 years, 5 months ago Modified 3 years, 5 months ago
visualization software - How to add a bond between two atoms in …
Jan 14, 2022 · 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 …
density functional theory - How to calculate homolytic bond ...
May 25, 2020 · An experimental colleague asked me how hard it would be to calculate homolytic bond-dissociation energies for different phosphonates which are involved in a …
Maximum bond length in Vesta - Matter Modeling Stack Exchange
Dec 30, 2022 · 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 …
Interpreting electron localization function (ELF) results
From the QTAIM analysis we got the the lead make a bond with one nitrogen atom at the nanostructure surface. This is due to the interbasin path together with the bond critical point …
How to canonicalize SMILES written with aromatic bond symbols (:)?
May 14, 2021 · I am using a package called PySmiles and it is returning a dialect of SMILES for aromatic groups that uses aromatic bond symbols e.g. NC:1:N:N:C:[N]1N. RDKit does not …