# Mindist usage on multichain systems

**URL:** <https://gromacs.bioexcel.eu/t/mindist-usage-on-multichain-systems/13455>\
**Category:** User discussions\
**Tags:** gmx-mindist\
**Created:** [May 11, 2026, 7:42am UTC](https://gromacs.bioexcel.eu/t/mindist-usage-on-multichain-systems/13455 "2026-05-11T07:42:48Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![csongor.nemeth](https://avatars.discourse-cdn.com/v4/letter/c/9de053/32.png) [@csongor.nemeth](https://gromacs.bioexcel.eu/u/csongor.nemeth)\
**Post date:** [May 11, 2026, 7:42am UTC](https://gromacs.bioexcel.eu/t/mindist-usage-on-multichain-systems/13455/1 "2026-05-11T07:42:48Z")

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GROMACS version: 2025.1  
GROMACS modification: Yes/No  
Hi Everyone!

I was using gmx mindist to check if a (large) number of simulations were done using an adequate box size. I was havinga. hard time to fix PBC and run the mindist on the trajectories when it comes to multichain proteins. Does anyone have any kind of experience with similar problems?

I was trying to fix PBC with the gmx, “trjconv”, “-s”, str(tpr),“-f”, str(xtc),c"-o", str(mol\_xtc), “-pbc”, “whole”, and also running gmx, “trjconv” “-s”, str(dummy\_tpr) “-f”, str(mol\_xtc) “-o”, str(tmp\_xtc) “-pbc”, “whole” “-center”, but it does not seem to see my protein complexes as a whole and will put cut the PBC at a wrong spot esenntially making mindist calculate the distance between the complexed proteins instead of the distance between complexes.

Thank you all for any help!