[gmx-users] Exclusions and pairs

Justin Lemkul jalemkul at vt.edu
Thu Jan 10 20:06:10 CET 2013

On 1/10/13 11:14 AM, Ignacio Fernández Galván wrote:
> 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]?

Pairs are bonded interactions.


The "type 3" pair you're referring to has a very specific use in free energy 
calculations, and that section of the manual has actually been re-written for 
version 4.6 and the usage changed to require a [pairs_nb] directive to indicate 
special nonbonded interactions in that case.  I think the newer explanation is 
slightly clearer than before.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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