# Regarding usage of -pbc yes while calculating mindist

**URL:** <https://gromacs.bioexcel.eu/t/regarding-usage-of-pbc-yes-while-calculating-mindist/13015>\
**Category:** User discussions\
**Created:** [December 5, 2025, 12:57pm UTC](https://gromacs.bioexcel.eu/t/regarding-usage-of-pbc-yes-while-calculating-mindist/13015 "2025-12-05T12:57:05Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![vangogh](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/vangogh/32/4841_2.png) [@vangogh](https://gromacs.bioexcel.eu/u/vangogh)\
**Post date:** [December 5, 2025, 12:57pm UTC](https://gromacs.bioexcel.eu/t/regarding-usage-of-pbc-yes-while-calculating-mindist/13015/1 "2025-12-05T12:57:05Z")

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GROMACS version: 2021.3  
GROMACS modification: Yes/No  
Hi, I am relatively new to MD simulations and needed a suggestion as to whether or not I should use -pbc yes while trying to calculate the minimum distance between my protein and its periodic image using gmx mindist?

After obtaining the raw trajectory, I have used gmx trjconv to make molecules whole, remove any jumps, and center the protein inside the box. Since, I have essentially corrected any PBC effects, do I still need to run gmx mindist with -pbc yes option?

Any help in this regard would actually be useful, I’m confused. Thank you in advance!