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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 experimental bond strengths for greater accuracy. The real bond length could be obtained by doing a CBS extrapolation using FCI-level calculations with aug-cc-pCV8Z and aug-cc-pCV9Z, then adding corrections for relativity, QED, Born-Oppenheimer breakdown, finite nuclear size effects, etc.) and perhaps calculating a full potential energy curve and solving the rovibrational Schroedinger equation ... What is the bond length of O2--? - Matter Modeling Stack Exchange I disagree with the statement by Tyberius that: "Bond order isn't terribly useful to a computationalist directly; however, it can be invaluable for translating Quantum Mechanical results into a framework thats readily understood by experimentalists.". Bond order quantifies the number of electrons that are shared (technically, 'dressed exchanged') between two atoms in a material. Bond order is ... reference request - Bond Order: When and how is it used today? - Matter ... 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 bond lengths from IR alone, you can likely develop a correlation between a particular IR frequency and bond length for a series of related compounds. 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. My question, broadly is: why is it harder to simulate a molecule with a stretched bond? Based on what I know so far, it seems the answer is: as the bond is stretched, multiple orbital energy levels converge in energy, and as a result, this yields exponentially many Slater determinants in the ground state with large coefficients. EDIT: I am going to post the derivation of the forces from this bond angle potential as presented by Swope and Ferguson 'Alternative Expressions for Energies and Forces Due to Angle Bending and Torsional Energy' 1992. I have xyz positions of my atoms in a .txt file, how can I extract information about bonding using VMD? I want to create a LAMMPS input file that contains not only the positions, but also informat...