[gmx-developers] Question about 1-4 interactions when using RB type dihedrals

Andrew DeYoung adeyoung at andrew.cmu.edu
Sat Dec 8 22:39:02 CET 2012


I am sorry to bother you on the developers list, but I am wondering if you
can please help me to understand the use of the [ pairs ] section with
respect to RB dihedrals, in an .itp file.

Page 130 of the version 4.5.4 manual says:

"[ dihedrals ] : in this case there are 9 proper dihedrals (funct = 1), 3
improper (funct = 2) and no Ryckaert-Bellemans type dihedrals. If you want
to include Ryckaert-Bellemans type dihedrals in a topology, do the following
(in case of e.g. decane):
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
1 2 3 4 3
2 3 4 5 3
and do not forget to ERASE THE 1-4 INTERACTION in [ pairs ]!"

My question is, why should erase the 1-4 interaction in [ pairs ] when using
RB type dihedrals? 

One user on the mailing list gave this response (
http://lists.gromacs.org/pipermail/gmx-users/2012-May/071346.html ):

"This is also a point I did not understand, when building the itp files for
my ionic liquids. I explicitly checked the influence and realized, that for
RB dihedrals the corresponding 1-4 interactions are only calculated, if the
respective atoms are listed in the pairs section. No matter how nexcl or
gen-pairs is set."

This is an intresting response, but it seems to say the opposite of what the
manual says.  The manual says that I should erase the 1-4 interaction in [
pairs ], but the user's response seems to suggest that  I should actually
include the 1-4 interaction in [ pairs ].

I am using OPLS-AA, and I would like to consider the 1-4 interaction at half
strength (i.e., fudgeQQ = 0.5 and fudgeLJ = 0.5), as the force field
prescribes.  So if I am using RB type dihedrals and I want to properly
include 1-4 interactions, do I include the 1-4 interactions in [ pairs ]?
Or do I exclude the 1-4 interactions in [ pairs ]?

Thank you SO much for your time!

Andrew DeYoung
Carnegie Mellon University

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