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What are the types of bond orders? - Matter Modeling Stack Exchange 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 ∇2ρ ∇ 2 ρ to characterize bonding 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
Scanning two bond lengths G-16 - Matter Modeling Stack Exchange 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 the case where you are scanning the bond lengths of C-Cl and C-H in chloromethane The code will first increment the bond length of C-Cl, and will then scan the C-H bond while keeping C-Cl bond constant This will result in a
Lost atoms in LAMMPS - Matter Modeling Stack Exchange 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
Simulating breaking bonds in molecular dynamics Very short answer: No, classical molecular dynamics cannot break bonds The potential you showed is the most common form of bond, the harmonic potential a k a Hookes law 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 As
Maximum bond length in Vesta - Matter Modeling Stack Exchange 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
How may I estimate the bond energy of a molecule? 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?
proteins - From a PDB file, how may I know which atoms have bonds . . . 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
How to perform charge analysis for a molecule I am doing dehydrogenation of a molecule (say CX12HX12 C X 12 H X 12) and I want to do charge analysis for dehydrogenated system (CX6HX6 C X 6 H X 6) How I can proceed? I can use Quantum ESPRESSO and Gaussian codes Also, I would be grateful, if you can advice me the physical significance of the charge analysis of a molecule
Is it possible to do a Gaussian redundant scan with some fixed bonds? The last line indicates that the bond (B) between atoms 5 and 6 are scanned (S) with 20 steps of size -0 1 Angstrom 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