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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
- 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
- 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
- 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?
- Measuring distance with ASE - Matter Modeling Stack Exchange
I think the answer to your problem lies in the CIF file With reference to the figure below, two out of four of the O neighbors of Cu are actually "the same atom" (only one of them is present as an entry in the unit cell and the other is a periodic image of the one in the unit cell) ASE's get_distance() and mic=True (Minimum Image Convention) works as expected, by only giving you the minimum
- Valence correction by adding formal charge in RDKit
I am modeling molecules as graphs, with nodes as atom types and edges as bond types (single, double, triple) I do not model formal charges or hydrogens explicitly (only heavy atoms) When trying to
- 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
- My CHARMM IC table generation has caused hydrogen to bond to two . . .
I am having issues with the alkyl hydrogens bonding to two carbons in a manner similar to the C-C bond I based my stream file on the all_36_lipid_detergents str file that comes with CHARMM, removing two carbons from lauric acid to create my decanoic acid stream file Does anybody have advice about how to fix my hydrogens?
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