# Extracting energy of ligand from md simulation

**URL:** <https://gromacs.bioexcel.eu/t/extracting-energy-of-ligand-from-md-simulation/5134>\
**Category:** User discussions\
**Created:** [October 31, 2022, 1:47am UTC](https://gromacs.bioexcel.eu/t/extracting-energy-of-ligand-from-md-simulation/5134 "2022-10-31T01:47:43Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![gweeish](https://avatars.discourse-cdn.com/v4/letter/g/a87d85/32.png) [@gweeish](https://gromacs.bioexcel.eu/u/gweeish)\
**Post date:** [October 31, 2022, 1:47am UTC](https://gromacs.bioexcel.eu/t/extracting-energy-of-ligand-from-md-simulation/5134/1 "2022-10-31T01:47:43Z")

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Hi, I have ran a MD simulation with a protein in a box of water molecules. I was wondering if it would be possible for me to extract the energies of just the protein, without contribution from water molecules.

Thank you.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [October 31, 2022, 2:17am UTC](https://gromacs.bioexcel.eu/t/extracting-energy-of-ligand-from-md-simulation/5134/2 "2022-10-31T02:17:41Z")

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You would have to extract the protein from the `.tpr` file with `gmx convert-tpr` and create a matching subset trajectory of protein-only coordinates with `gmx trjconv`, then use `mdrun -rerun` to recalculate energies. There is no point in doing this as the energy is not physically meaningful.