# Large differences in gmx mindist values with and without PBC correction

**URL:** <https://gromacs.bioexcel.eu/t/large-differences-in-gmx-mindist-values-with-and-without-pbc-correction/12975>\
**Category:** User discussions\
**Created:** [November 25, 2025, 10:53am UTC](https://gromacs.bioexcel.eu/t/large-differences-in-gmx-mindist-values-with-and-without-pbc-correction/12975 "2025-11-25T10:53:28Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Devid](https://avatars.discourse-cdn.com/v4/letter/d/22d042/32.png) [@Devid](https://gromacs.bioexcel.eu/u/Devid)\
**Post date:** [November 25, 2025, 10:53am UTC](https://gromacs.bioexcel.eu/t/large-differences-in-gmx-mindist-values-with-and-without-pbc-correction/12975/1 "2025-11-25T10:53:28Z")

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Dear users,  
I simulated a protein for 1 µs and calculated the minimum distance using:

gmx mindist -s .tpr -f .xtc -od mindist.xvg -n .ndx

I computed mindist on the raw trajectory and again after applying PBC corrections, but the results differ substantially. As far as I understand, mindist should be the same after GROMACS’ automatic corrections. Can anyone help me understand why I see such large differences?

Thanks

Devid

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [November 25, 2025, 12:42pm UTC](https://gromacs.bioexcel.eu/t/large-differences-in-gmx-mindist-values-with-and-without-pbc-correction/12975/2 "2025-11-25T12:42:52Z")

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What do you mean with “after applying PBC corrections”?

gmx mindist should always produce correct distances.

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<div class="post-metadata">

**Author:** ![Devid](https://avatars.discourse-cdn.com/v4/letter/d/22d042/32.png) [@Devid](https://gromacs.bioexcel.eu/u/Devid)\
**Post date:** [November 25, 2025, 12:50pm UTC](https://gromacs.bioexcel.eu/t/large-differences-in-gmx-mindist-values-with-and-without-pbc-correction/12975/3 "2025-11-25T12:50:49Z")

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Hii @hess

Thanks for your reply.

I mean that I calculated the mindist using two trajectory (.xtc) files:

1. The raw trajectory resulted from the MD simulation and
2. The trajectory after centering the protein and fitting the backbone

and I am getting different results in the two cases.

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [November 25, 2025, 1:02pm UTC](https://gromacs.bioexcel.eu/t/large-differences-in-gmx-mindist-values-with-and-without-pbc-correction/12975/4 "2025-11-25T13:02:53Z")

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Fitting rotates the structure, then the trajectory is no longer compatible with the box.

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<div class="post-metadata">

**Author:** ![Devid](https://avatars.discourse-cdn.com/v4/letter/d/22d042/32.png) [@Devid](https://gromacs.bioexcel.eu/u/Devid)\
**Post date:** [November 25, 2025, 1:16pm UTC](https://gromacs.bioexcel.eu/t/large-differences-in-gmx-mindist-values-with-and-without-pbc-correction/12975/5 "2025-11-25T13:16:24Z")

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I also tested the centered trajectory (.xtc) without fitting, but the results are still different compared to the raw trajectory from the MD simulation.

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [November 25, 2025, 3:08pm UTC](https://gromacs.bioexcel.eu/t/large-differences-in-gmx-mindist-values-with-and-without-pbc-correction/12975/6 "2025-11-25T15:08:25Z")

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That is strange. Translated doesn’t affect distances.