# PBC correction while inserting a molecule

**URL:** <https://gromacs.bioexcel.eu/t/pbc-correction-while-inserting-a-molecule/8337>\
**Category:** User discussions\
**Created:** [February 15, 2024, 4:55am UTC](https://gromacs.bioexcel.eu/t/pbc-correction-while-inserting-a-molecule/8337 "2024-02-15T04:55:09Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![mjm91](https://avatars.discourse-cdn.com/v4/letter/m/54ee81/32.png) [@mjm91](https://gromacs.bioexcel.eu/u/mjm91)\
**Post date:** [February 15, 2024, 4:55am UTC](https://gromacs.bioexcel.eu/t/pbc-correction-while-inserting-a-molecule/8337/1 "2024-02-15T04:55:09Z")

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Dear gromacs users,

I am currently working with polymer and studying the effect on a protein. I am generating the polymer configuration and protein configuration separately. So I am equilibrating the protein and the polymer in water for long time and then extract the polymer configuration and inserting in the protein using gmx insert-molecules by replacing water molecules.

For this purpose I am removing PBC from the final gro file obtained for the protein-in-water equilibration simulation (pbc\_protein\_water.gro) and removing PBC from the final gro file obtained for the polymer-in-water equilibration simulation and extracting polymer coordinates only (pbc\_polymer.gro), making sure there is no broken molecule or outside boundary as that might have an effect while using gmx insert-molecules. Then I am inserting the pbc\_polymer.gro into the pbc\_protein\_water.gro by using the gmx insert-molecules tool by replacing water molecules. Is this fine or we don’t need to remove PBC for preparing the initial configuration for the protein-polymer-water system?

Any suggestion(s) is much appreciated.