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 …

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 …

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 …

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 …

I was wondering if there were any reliable algorithms out there that could allocate bond orders and formal charges of a given molecular structure if just the atomic coordinates (x,y,z) and atom typ...

I am conducting a study to compute the bond potentials/energies of elemental, binary, and ternary semiconductors using DFT within the Quantum Espresso software package or any other …

2022年11月9日 · Given the SMILES of my molecule, how can I get a weighted adjacency matrix where the weights are the bond lengths, using the Rdkit package and Python?

2023年9月29日 · +1, but we only allow 1 question/post. Also, can you provide a sample from one of your actual PDB files? Generally when you are given XYZ coordinates of a molecule (e.g. a …

2022年2月12日 · I have just started working with VMD, and I figured out how to generate a Carbon Nano Tube (CNT) in VMD and save it's atom positions to use as initial file in …

2022年1月14日 · Thank you for your comment. This method is ok now, but why VMD didn't draw the bond in the visualization. I have the two atoms without a bond between.