|
- 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 $\nabla^2\rho$ to characterize bonding 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
- How may I calculate the bond length between two atoms?
Bond formation could be something like 1-P break b r e a k You could also run quantum calculations for all possible pairs (or higher order clusters) of atoms or hit the literature to look up experimental bond strengths for greater accuracy
- 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
- 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
- Generate structure using atomic coordinates - Matter Modeling Stack . . .
10 To understand the new coordinates after altering the bond length of the C-O bonds you can use the below approach: Let us first visualize the positions of all the atoms before and after altering the bond length: The atoms with * are the atoms at the new coordinates after bond altering So imagine a vector from the O atom to the C atom
- Number of hydrogen bonds - Matter Modeling Stack Exchange
I'm studying hydrogen bonds in a water system The commonly accepted parameters are: D-A distance = 3 5 Å and H-D-A angle = 30° To analyze the hydrogen bonds, I plotted the number of hydrogen bond
- 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
|
|
|