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  1. What is the method to examine atomic bonds and hydrogen …

    2025年5月1日 · Bond path can be straight line or curve, obviously for the latter case the length of bond path is longer than the sum of the distances between BCP and associated two (3,-3) CPs. If you are …

  2. How may I calculate the bond length between two atoms?

    2021年4月26日 · 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 literature to look up …

  3. How may I estimate the bond energy of a molecule?

    2025年2月20日 · 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 …

  4. Bond length from infrared spectra? - Matter Modeling Stack Exchange

    2020年7月26日 · If you know the bond lengths of few such compounds, you can derive a very accurate linear correlation between the bond length and the frequency. So while you can't directly predict …

  5. Lost atoms in LAMMPS - Matter Modeling Stack Exchange

    2022年11月1日 · 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 …

  6. Number of hydrogen bonds - Matter Modeling Stack Exchange

    2024年8月26日 · 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 …

  7. How to carry out BSSE correction in ORCA?

    2025年1月22日 · 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 …

  8. proteins - From a PDB file, how may I know which atoms have bonds ...

    2023年9月29日 · 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 …

  9. Is it possible to do a Gaussian redundant scan with some fixed bonds?

    2021年6月18日 · 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 …

  10. Maximum bond length in Vesta - Matter Modeling Stack Exchange

    2022年12月30日 · 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 …