# Inconsistent shifts during trjconv **URL:** \ **Category:** User discussions\ **Created:** [December 1, 2021, 2:02pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238 "2021-12-01T14:02:16Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![roshanshrestha](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/roshanshrestha/32/515_2.png) [@roshanshrestha](https://gromacs.bioexcel.eu/u/roshanshrestha)\ **Post date:** [December 1, 2021, 2:02pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/1 "2021-12-01T14:02:16Z")
GROMACS version: 2020.5 GROMACS modification: Yes/No While treating pbc using **gmx trjconv -s prod.tpr -f prod.xtc -o nopbc.xtc -pbc mol -center** , gromacs throws me these warnings and so on - > There were 162 inconsistent shifts. Check your topology > There were 162 inconsistent shifts. Check your topology > There were 162 inconsistent shifts. Check your topology time 100.000 > There were 162 inconsistent shifts. Check your topology > There were 162 inconsistent shifts. Check your topology time 200.000 > There were 162 inconsistent shifts. Check your topology What’s the issue in here, and how can I rectify it? Thank you. ---
**Author:** ![mulpurinagaraju](https://avatars.discourse-cdn.com/v4/letter/m/8e7dd6/32.png) [@mulpurinagaraju](https://gromacs.bioexcel.eu/u/mulpurinagaraju)\ **Post date:** [January 12, 2022, 8:22pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/2 "2022-01-12T20:22:01Z")
I am also getting the same message. There were 52 inconsistent shifts. Check your topology please let me know if you resolve it. ---
**Author:** ![roshanshrestha](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/roshanshrestha/32/515_2.png) [@roshanshrestha](https://gromacs.bioexcel.eu/u/roshanshrestha)\ **Post date:** [January 14, 2022, 1:50pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/3 "2022-01-14T13:50:34Z")
Sorry, I haven’t actually. Gromacs is throwing out same error to me. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 14, 2022, 6:16pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/4 "2022-01-14T18:16:09Z")
What is the system? Is it some kind of infinite molecule like a CNT? The topic gets discussed very often (lots of info from the old mailing list as well as this forum, e.g. [Inconsistent shifts](https://gromacs.bioexcel.eu/t/inconsistent-shifts/756)) ---
**Author:** ![mulpurinagaraju](https://avatars.discourse-cdn.com/v4/letter/m/8e7dd6/32.png) [@mulpurinagaraju](https://gromacs.bioexcel.eu/u/mulpurinagaraju)\ **Post date:** [January 17, 2022, 11:34pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/5 "2022-01-17T23:34:59Z")
Thank you very much for your response. My system has two graphene sheets and water molecules. ---
**Author:** ![mulpurinagaraju](https://avatars.discourse-cdn.com/v4/letter/m/8e7dd6/32.png) [@mulpurinagaraju](https://gromacs.bioexcel.eu/u/mulpurinagaraju)\ **Post date:** [January 17, 2022, 11:41pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/6 "2022-01-17T23:41:46Z")
Hi Jalemkul, My system has graphene sheets and water molecules. Graphene sheets as one group and water molecules as the second group. I want to calculate only water molecule pressure in X, Y, Z directions. How to calculate it? I used \*\*gmx traj \*\* command to extract force but it is not working. I used \*\* gmx energy \*\* it gives whole system pressure. Any help is appreciated. Thank you very much. Best regards, Nagaraju ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 18, 2022, 4:20am UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/7 "2022-01-18T04:20:33Z")
> [@mulpurinagaraju](#): > > Thank you very much for your response. My system has two graphene sheets and water molecules. In this case, there is not a single solution to wrapping your molecule given its periodic, infinite nature. The warnings are not necessarily problematic but perhaps a more judicious choice of group for centering (a subset of atoms that can serve as a suitable reference) is appropriate. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 18, 2022, 4:21am UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/8 "2022-01-18T04:21:19Z")
> [@mulpurinagaraju](#): > > I want to calculate only water molecule pressure in X, Y, Z directions. How to calculate it? I don’t think such a quantity makes sense. You can’t have “pressure of only water” because the interactions among water molecules depend on collisions with the graphene, which contributes to the virial. ---
**Author:** ![mulpurinagaraju](https://avatars.discourse-cdn.com/v4/letter/m/8e7dd6/32.png) [@mulpurinagaraju](https://gromacs.bioexcel.eu/u/mulpurinagaraju)\ **Post date:** [January 18, 2022, 3:41pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-during-trjconv/3238/9 "2022-01-18T15:41:31Z")
Thank you very much for your information. My system has water molecules between two graphene sheets. I would like to measure the pressure of water on graphene sheets. According to pressure, I will reduce water molecules to get desired pressure (certain range, ex: 0-200 bar) in the NVT ensemble. Thank you very much. Have a nice day! Best, Nagaraju