[gmx-users] Intramolecular interactions

[Robson da Silva]

Dear gmx users, I have a question: how the program generates the
intramolecular interactions? I mean, how the program recognizes the 1-2,
1-3 and 1-4 bonds between the atoms in the same molecule?

I'm asking this because I'm developing a program and I can generate the
intramolecular interactions if I specified the bonds in the .itp file but
when I don't have bonds specified, I can't generate them. How the program
does that?

Best,
Robson.

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Robson da Silva
mail: rooliboni at gmail.com
MSc. in Chemistry
Universidade Federal de Santa Catarina - UFSC
Department of Chemistry
Campus Universitario
CEP 88040-900
Florianópolis, Santa Catarina - Brazil.