# Dummy atoms **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [June 12, 2023, 8:22am UTC](https://gromacs.bioexcel.eu/t/dummy-atoms/6592 "2023-06-12T08:22:15Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![sknippen](https://avatars.discourse-cdn.com/v4/letter/s/f05b48/32.png) [@sknippen](https://gromacs.bioexcel.eu/u/sknippen)\ **Post date:** [June 12, 2023, 8:22am UTC](https://gromacs.bioexcel.eu/t/dummy-atoms/6592/1 "2023-06-12T08:22:15Z")
GROMACS version: 2019.4 GROMACS modification: No Hi everybody, Willing to use dummy atoms (e.g. definition of O2 with O-dummy-O) in a polymer membrane, I have difficulties to minimize the structure (the forces on the dummy atom are too large). There must be something wrong with my construction. I defined - in ffbonded.itp: OM OM 1 0.12440 347286.6 - in ffnonbonded.itp : opls\_972 OM 8 15.99940 0.000 A 3.58000e-01 9.81100e-01 DUO DU 0 0.00000 0.8476 D 0.00000e+00 0.00000e+00 - in O2M.top: – [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 O2M rtp O2M q 0.0 1 opls\_972 1 O2M O1 1 -0.4238 15.9994 2 DUO 1 O2M DU 1 0.8476 0 3 opls\_972 1 O2M O2 1 -0.4238 15.9994 ; qtot 0 [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 O2M rtp O2M q 0.0 1 opls\_972 1 O2M O1 1 -0.4238 15.9994 2 DUO 1 O2M DU 1 0.8476 0 3 opls\_972 1 O2M O2 1 -0.4238 15.9994 ; qtot 0 [bonds] ; ai aj funct c0 c1 c2 c3 1 3 1 [dummies2] 2 1 3 1 0.5 [constraints] 1 3 1 1.2 ## [exclusions] 1 2 3 I assume the problem is related to ‘dummies2’, ‘constraints’ and ‘exclusions’. What is it that I don’t understand? Thanks, Stefan ---
**Author:** ![sknippen](https://avatars.discourse-cdn.com/v4/letter/s/f05b48/32.png) [@sknippen](https://gromacs.bioexcel.eu/u/sknippen)\ **Post date:** [June 14, 2023, 9:03am UTC](https://gromacs.bioexcel.eu/t/dummy-atoms/6592/2 "2023-06-14T09:03:07Z")
The right construction is the following: – [moleculetype] ; Name nrexcl O2M 3 [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 O2M rtp O2M q 0.0 1 opls\_972 1 O2M O1 1 -0.4238 15.9994 2 opls\_972 1 O2M O2 1 -0.4238 15.9994 ; qtot 0 3 DUO 1 O2M DU 1 0.8476 0 ; qtot 0 [bonds] ; ai aj funct c0 c1 c2 c3 1 2 1 [dummies2] 3 1 2 1 0.5 ## [exclusions] 1 2 3 3 1 2 2 1 3 Maybe a small note: ‘dummies2’ is depreciated - the keyword (with the same functions) ‘virtual\_sites2’ is advocated nowadays. The manual (Fig. 34 in [Methods — GROMACS 2019-rc1 documentation](https://manual.gromacs.org/documentation/2019-rc1/reference-manual/functions/interaction-methods.html#virtualsites) ) gives numerator ‘2’ to a linear construction of a dummy atom. However, in ‘[dummies2]’ (or ‘[virtual\_sites2]’) still ‘1’ is used (the last ‘1’ in 3 1 2 1 0.5 )