# Gmx trjconv -pbc whole error

**URL:** <https://gromacs.bioexcel.eu/t/gmx-trjconv-pbc-whole-error/1348>\
**Category:** User discussions\
**Created:** [December 28, 2020, 7:51pm UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-pbc-whole-error/1348 "2020-12-28T19:51:46Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![L\_k](https://avatars.discourse-cdn.com/v4/letter/l/ebca7d/32.png) [@L\_k](https://gromacs.bioexcel.eu/u/L_k)\
**Post date:** [December 28, 2020, 7:51pm UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-pbc-whole-error/1348/1 "2020-12-28T19:51:46Z")

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Hello All,

I have been processing some trajectory files by removing pbc, which often requires a sequence of gmx trjconv steps. This time, my protein appears split in three pieces, and after applying whole there are still two halves. Then, if I apply cluster or nojump there is a clear split down the center of the molecule which seems to be causing an increase in rmsd values. If anyone has experienced this or has a suggestion on how to resolve this, I would greatly appreciate it.

Thank you!

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [January 7, 2021, 6:05pm UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-pbc-whole-error/1348/2 "2021-01-07T18:05:16Z")

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Hi L\_k,

just a guess - are you using the `tpr` file for the `-s` option when using `whole`? Otherwise `trjconv` still gives you a result, but cannot make the structure whole.

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<div class="post-metadata">

**Author:** ![L\_k](https://avatars.discourse-cdn.com/v4/letter/l/ebca7d/32.png) [@L\_k](https://gromacs.bioexcel.eu/u/L_k)\
**Post date:** [January 7, 2021, 6:17pm UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-pbc-whole-error/1348/3 "2021-01-07T18:17:29Z")

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Hi cblau,

Thank you for your reply. Yes, I supply the original run tpr file with -s.