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.
http://lists.gromacs.org/pipermail/gmx-users/2009-July/043326.html
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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