# Calculation of Interaction energies **URL:** \ **Category:** User discussions\ **Created:** [February 23, 2026, 5:54am UTC](https://gromacs.bioexcel.eu/t/calculation-of-interaction-energies/13235 "2026-02-23T05:54:38Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Pbagchi](https://avatars.discourse-cdn.com/v4/letter/p/df705f/32.png) [@Pbagchi](https://gromacs.bioexcel.eu/u/Pbagchi)\ **Post date:** [February 23, 2026, 5:54am UTC](https://gromacs.bioexcel.eu/t/calculation-of-interaction-energies/13235/1 "2026-02-23T05:54:39Z")
GROMACS version: 2021 GROMACS modification: No Hello! I have a system containing a membrane and two proteins. I would like to compute the interaction energies: - between the membrane and Protein 1 - between the membrane and Protein 2 - between Protein 1 and Protein 2 I am unsure about the best approach. One option I considered is generating separate trajectories for each pair of components, rerunning the energy calculation, and comparing their potential energies. Alternatively, I could define energy groups for the full system and extract: - LJ-SR interactions - Coul-SR interactions However, I am concerned that this method only includes non-bonded interactions. Could someone advise which approach is more appropriate and commonly used for estimating interaction energies in such systems? Thank you in advance! ---
**Author:** ![daviddesancho](https://avatars.discourse-cdn.com/v4/letter/d/cdc98d/32.png) [@daviddesancho](https://gromacs.bioexcel.eu/u/daviddesancho)\ **Post date:** [February 24, 2026, 4:09pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-interaction-energies/13235/2 "2026-02-24T16:09:45Z")
You do not need to define separate trajectories. Instead, you can rerun to recalculate energies for the relevant energy groups. These can be defined using an index (`ndx`) file, although this may be not even needed, depending on your topology. If you include the desired sets of `energy-grps` in the `mdp` file, generate a new `tpr` file and then run `gmx mdrun -rerun` with the new `tpr` file, you should be able to get what you want in the energy (`edr`) file. A [note of warning](https://gromacs.bioexcel.eu/t/energy-interaction-between-two-groups/9827) however from a previous question. And also, I am assuming your groups are covalently bonded, so non-bonded interactions are all there is. I hope this helps, David ---
**Author:** ![dspoel](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dspoel/32/64_2.png) [@dspoel](https://gromacs.bioexcel.eu/u/dspoel)\ **Post date:** [February 25, 2026, 7:16am UTC](https://gromacs.bioexcel.eu/t/calculation-of-interaction-energies/13235/3 "2026-02-25T07:16:07Z")
If you want to go beyond interaction energy, check out the recipe in this old paper (details in SI). [https://pubs.acs.org/doi/10.1021/ct400404q](https://pubs.acs.org/doi/10.1021/ct400404q) ---
**Author:** ![Pbagchi](https://avatars.discourse-cdn.com/v4/letter/p/df705f/32.png) [@Pbagchi](https://gromacs.bioexcel.eu/u/Pbagchi)\ **Post date:** [February 25, 2026, 7:36am UTC](https://gromacs.bioexcel.eu/t/calculation-of-interaction-energies/13235/4 "2026-02-25T07:36:55Z")
Thanks @daviddesancho and @dspoel ---
**Author:** ![Pbagchi](https://avatars.discourse-cdn.com/v4/letter/p/df705f/32.png) [@Pbagchi](https://gromacs.bioexcel.eu/u/Pbagchi)\ **Post date:** [March 2, 2026, 9:50am UTC](https://gromacs.bioexcel.eu/t/calculation-of-interaction-energies/13235/5 "2026-03-02T09:50:28Z")
Just a quick check: when extracting interaction energies using **gmx energy** , the values are reported in kJ/mol, correct? There isn’t any case where they appear as kJ/mol but are actually in J/mol, right? ---
**Author:** ![dspoel](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dspoel/32/64_2.png) [@dspoel](https://gromacs.bioexcel.eu/u/dspoel)\ **Post date:** [March 30, 2026, 12:23pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-interaction-energies/13235/6 "2026-03-30T12:23:04Z")
Correct, except for temperature, pressure etc.