[gmx-developers] Question about 1-4 interactions when using RB type dihedrals
David van der Spoel
spoel at xray.bmc.uu.se
Sun Dec 9 09:40:30 CET 2012
On 2012-12-08 22:39, Andrew DeYoung wrote:
> 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
The remark about removing 1-4 interaction *only* is need for alkane
chains, if you want to use the original RB dihedrals. These are still
used in some lipid force fields. However for most cases we use RB
dihedrals as a sum of cosines (e.g. in OPLS or Amber) and in this case
the rules that hold for the those force fields should be applied.
Seems that we need to update the manual (and I just did).
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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