# Energy groups find self interacting Na+ and Cl+ for Coulombic interaction energy? **URL:** \ **Category:** User discussions\ **Created:** [March 27, 2023, 1:09pm UTC](https://gromacs.bioexcel.eu/t/energy-groups-find-self-interacting-na-and-cl-for-coulombic-interaction-energy/6052 "2023-03-27T13:09:02Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![aapo2002](https://avatars.discourse-cdn.com/v4/letter/a/a87d85/32.png) [@aapo2002](https://gromacs.bioexcel.eu/u/aapo2002)\ **Post date:** [March 27, 2023, 1:09pm UTC](https://gromacs.bioexcel.eu/t/energy-groups-find-self-interacting-na-and-cl-for-coulombic-interaction-energy/6052/1 "2023-03-27T13:09:02Z")
GROMACS version:2022v2 GROMACS modification: No Hi, I am trying to calculate the Coulombic interaction energy between a single Na+ and Cl- ions. Using experimental distance of 0.276 nm, I can calculate 503 kJ/mol from the simple coulombic potential energy equation. ## When I try to calculate the same by Gromacs using energy groups, it gives me the following output. Energy Average Err.Est. RMSD Tot-Drift Coulomb (SR) -563.928 – 0 0 (kJ/mol) Coul. recip. 60.4996 – 0 0 (kJ/mol) Potential -489.701 – 0 0 (kJ/mol) Coul-SR:S1-S1 -204.026 – 0 0 (kJ/mol) LJ-SR:S1-S1 0 – 0 0 (kJ/mol) Coul-SR:S1-S2 -155.875 – 0 0 (kJ/mol) LJ-SR:S1-S2 13.7274 – 0 0 (kJ/mol) Coul-SR:S2-S2 -204.026 – 0 0 (kJ/mol) LJ-SR:S2-S2 0 – 0 0 (kJ/mol) So it looks like when creating energy groups, it finds self interaction terms of Na+Na+ and Cl- I am using Verlet cutoff scheme (unfortunately group option is deprecated). Is it interacting with periodic images? Since the new versions do not allow other than Verlet cutoff scheme and Verlet only works with pbc, I could not test it on 2022 v 2. ## But I have installed Gromacs 2018 and tried on that with pbc=no and cutoff-scheme=group with all cutoffs and nstlist stting to 0. It does not produce any artificial interaction and produces the interaction correctly: Energy Average Err.Est. RMSD Tot-Drift LJ (SR) 13.7274 – 0 0 (kJ/mol) Coulomb (SR) -503.389 – 0 0 (kJ/mol) Potential -489.662 – 0 0 (kJ/mol) Coul-SR:S1-S1 0 – 0 0 (kJ/mol) LJ-SR:S1-S1 0 – 0 0 (kJ/mol) Coul-SR:S1-S2 -503.389 – 0 0 (kJ/mol) LJ-SR:S1-S2 13.7274 – 0 0 (kJ/mol) Coul-SR:S2-S2 0 – 0 0 (kJ/mol) LJ-SR:S2-S2 0 – 0 0 (kJ/mol) ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [March 28, 2023, 9:07am UTC](https://gromacs.bioexcel.eu/t/energy-groups-find-self-interacting-na-and-cl-for-coulombic-interaction-energy/6052/2 "2023-03-28T09:07:00Z")
You seem to be using PME in the first case and not in the second, so these are completely different calculations. PME computes periodic Coulomb interactions. ---
**Author:** ![aapo2002](https://avatars.discourse-cdn.com/v4/letter/a/a87d85/32.png) [@aapo2002](https://gromacs.bioexcel.eu/u/aapo2002)\ **Post date:** [March 28, 2023, 10:20am UTC](https://gromacs.bioexcel.eu/t/energy-groups-find-self-interacting-na-and-cl-for-coulombic-interaction-energy/6052/3 "2023-03-28T10:20:43Z")
Thanks for your reply. That is my bad. Yes, you are right, I used pme. Using cutoff instead mostly fixed the problem. But, i still get artificial self-self interactions unless I give really long cutoffs. I tried 180 nm but still small self interaction. Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Coulomb (SR) -503.391 – 0 0 (kJ/mol) Potential -489.663 – 0 0 (kJ/mol) Coul-SR:S1-S1 -3.838 – 0 0 (kJ/mol) LJ-SR:S1-S1 0 – 0 0 (kJ/mol) Coul-SR:S1-S2 -495.715 – 0 0 (kJ/mol) LJ-SR:S1-S2 13.728 – 0 0 (kJ/mol) Coul-SR:S2-S2 -3.838 – 0 0 (kJ/mol) LJ-SR:S2-S2 0 – 0 0 (kJ/mol) ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [March 28, 2023, 11:00am UTC](https://gromacs.bioexcel.eu/t/energy-groups-find-self-interacting-na-and-cl-for-coulombic-interaction-energy/6052/4 "2023-03-28T11:00:23Z")
I think you should get what you want when you set coulomb-modifier=none ---
**Author:** ![aapo2002](https://avatars.discourse-cdn.com/v4/letter/a/a87d85/32.png) [@aapo2002](https://gromacs.bioexcel.eu/u/aapo2002)\ **Post date:** [March 29, 2023, 9:44pm UTC](https://gromacs.bioexcel.eu/t/energy-groups-find-self-interacting-na-and-cl-for-coulombic-interaction-energy/6052/5 "2023-03-29T21:44:42Z")
Thanks a lot. That solved my problem. I am currently working on charged vs non charged groups and would like to get electrostatic interaction of groups as good as possible. So using pme, and any switching is not good for at least being on the same page with my own script, Amber or other software comparsion. I see you had already mention that point on the mdp options help page :“coulomb-modifier=none: This can be useful when comparing energies with those computed with other software.” Thanks a lot for your help. ---
**Author:** ![Sourav7](https://avatars.discourse-cdn.com/v4/letter/s/ba9def/32.png) [@Sourav7](https://gromacs.bioexcel.eu/u/Sourav7)\ **Post date:** [May 1, 2025, 10:21am UTC](https://gromacs.bioexcel.eu/t/energy-groups-find-self-interacting-na-and-cl-for-coulombic-interaction-energy/6052/6 "2025-05-01T10:21:52Z")
when i am calculating NA-NA interaction in my system why i am getting negative value for coulomb interaction. ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [May 2, 2025, 8:01am UTC](https://gromacs.bioexcel.eu/t/energy-groups-find-self-interacting-na-and-cl-for-coulombic-interaction-energy/6052/7 "2025-05-02T08:01:51Z")
I answered this question in another thread. The V\_0 term of PME (see reference manual) is added to the SR energy component. V\_0 is always negative.