Hello, I was following the hexane hybrid tutorial and there [exclusions] were included in the topology file to consider only non-bonded forces for subsequent force-matching. I a bit confused about how exclusions work since in the GROMACS manual (Chap. 5 Topologies) it is said that the [exclusions] section will exclude all the non-bonded interactions between the atom indices listed. It sounded like the opposite of what was intended in the hybrid hexane. I am clearly missing something. I would appreciate if someone can help me to understand it. Thanks.
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