[gmx-users] Exclusions and pairs

Ignacio Fernández Galván jellby at yahoo.com
Thu Jan 10 17:14:48 CET 2013

Dear Gromacs users:

Am I right assuming that [exclusions] do not affect the interactions defined by [pairs]?

This seems to be implied from the note in section 5.3.4 in the manual: "Note that one should add exclusions for all atom pairs participating in pair interactions type 3, otherwise such pairs will also end up in the normal neighbor lists".

I think, however, that it can be confusing given the overall concept: [exclusions] removes non-bonded interactions, and [pairs] defines non-bonded interactions. One could think that pairs would be excluded too. May I suggest a more explicit statement to be added to the 5.4 sections (that [exclusions] do not affect [pairs]?


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