Can anyone recommend a good code/software/implementation to identify the change of molecules (bond creation/break, number of molecules at a given timestep, etc.)? I am currently working with XYZ XDATCAR PDB LAMMPS data files.
Thank you!
Martin Klvana
In molecular dynamics simulation, bond formation/breakage is either intentional (hence known beforehand) or unintentional (explosion) -- which of the two is your case?
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Hashan Peiris
Martin Klvana I am sorry but I do not fully understand what you mean by the "unintentional (explosion)" type. However, most of the calculations are AIMD trajectories calculated using VASP. Does that answer your question?
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Przemyslaw Dziegielewski
OVITO - recognize xyz, lammps dump files and another. The basic version is for free.
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