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How to carry out BSSE correction in ORCA? 2 I'm working on a diatomic molecule and need to accurately describe its bond dissociation energy I plan to perform BSSE correction (Counterpoise or some other) for this molecule While Gaussian handles this in a single step, I'm struggling with how to carry out this correction in ORCA
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
density functional theory - What is the difference between relax and . . . For very simple systems and tasks, such as optimizing the bond length of a diatomic molecule, it is straightforward to parameterize the geometry in terms of a single interatomic distance, and do multiple SCFs on your own at different interatomic distances to get a simple two-dimensional energy-interatomic distance plot to visualize the
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
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 to use rigid scan with dummy atoms in gaussian? For simplicity, I want to increase the bond lengths between the dummy atom and one O atom (I require a more complex scan) Here is my gaussian input, %chk=scan_test chk # scan hf 3-21g Title Card Required 0 1 X O 1 R1 H 1 R2 2 A1 H 1 R3 2 A2 3 D1
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
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