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I wonder if there exists a tool/script/algorithm to identify multiple molecules and/or atoms in a single XYZ or gaussian log file.

As an example, imagine one does a single point calculation for the ethanol-$\ce{Cl2}$ system, where the two molecules are placed next to each other at some distance. If one wants to detect all participating entities (be it molecules or atoms) what would be the best approach?

Could we use "standard" bond lengths between atoms and atoms allowed max number of bonds to do that? I suspect the problem is much more complicated than that.

Nisarg Bhavsar
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Daniel
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    Yes, you have stumbled upon the fact that there is no unique physical/mathematical definition of a molecule. The same goes for bonds. Nothing stops me from considering a dimer as a single entity. In the calculation it is even treated as such. But as you realized, you can make up your own definitions and check for them. If you know or assume that you have certain monomers that are retained, you can check for them. But you need to define them in some way. Using a distance as bond length and checking all atom pair distances for it is a possibility. Many visualization tools work that way. – Hans Wurst May 14 '21 at 08:19

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