# Find error while using trjconv **URL:** \ **Category:** User discussions\ **Created:** [September 23, 2024, 12:42pm UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215 "2024-09-23T12:42:48Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Munazzah1](https://avatars.discourse-cdn.com/v4/letter/m/50afbb/32.png) [@Munazzah1](https://gromacs.bioexcel.eu/u/Munazzah1)\ **Post date:** [September 23, 2024, 12:42pm UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215/1 "2024-09-23T12:42:48Z")
GROMACS version:2022.5-plumed\_2.9.0 GROMACS modification: Yes/No Hello developers, I am simulation a long IDP with 58 residues. But when use the command gmx trjconv -f production.xtc -n index.ndx -o trajout.xtc -pbc whole -center -s production.tpr It gives me following error: Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 790 atoms. The longest distance involved in such interactions is 9.511 nm which is above half the box length. This molecule type consists of muliple parts, e.g. monomers, that are connected by interactions that are not chemical bonds, e.g. restraints. Such systems can not be treated. The only solution is increasing the box size. I choose the box size of 3 nm. Please guide me why this issue occure. Thanks in Advance. Regards, Munazzah PhD student ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 24, 2024, 8:58am UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215/2 "2024-09-24T08:58:45Z")
I would think that the error is from the `-center` option. Try without it and see if it works. If it does, you might want to select only a few atoms, for centering, close to where you want to center instead of selecting the whole molecule. ---
**Author:** ![Munazzah1](https://avatars.discourse-cdn.com/v4/letter/m/50afbb/32.png) [@Munazzah1](https://gromacs.bioexcel.eu/u/Munazzah1)\ **Post date:** [September 24, 2024, 12:17pm UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215/3 "2024-09-24T12:17:04Z")
Hello Sir, Thanks for reply. I used the command without -center option but i am facing the same error again. ![Screenshot from 2024-09-24 17-39-58](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/341d170923a1eca18016dd82f1ee7512a9d6b301.png) ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 24, 2024, 12:45pm UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215/4 "2024-09-24T12:45:06Z")
Does it work if you use `-pbc nojump` instead of `-pbc whole`? ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 24, 2024, 12:49pm UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215/5 "2024-09-24T12:49:42Z")
By the way, according to the selections, there are 739 atoms in the protein. The error says that there are 790 atoms in the molecule type. Are the ions somehow included in the same molecule type as the protein? Could you post your topology (.top) file? You might have to rename it to, e.g., .txt. ---
**Author:** ![Munazzah1](https://avatars.discourse-cdn.com/v4/letter/m/50afbb/32.png) [@Munazzah1](https://gromacs.bioexcel.eu/u/Munazzah1)\ **Post date:** [September 24, 2024, 1:05pm UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215/7 "2024-09-24T13:05:58Z")
Yes, it was working with -pbc nojump. I am also attaching the topology file. [topol.txt](https://gromacs.bioexcel.eu/uploads/short-url/h4R3fVKKod86Y23LoVLVXXw9g4t.txt) (371.3 KB) ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 24, 2024, 1:16pm UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215/8 "2024-09-24T13:16:57Z")
Good to hear that that worked. Does it look OK if you visualize it? I can’t see anything strange in the topology file. ---
**Author:** ![Munazzah1](https://avatars.discourse-cdn.com/v4/letter/m/50afbb/32.png) [@Munazzah1](https://gromacs.bioexcel.eu/u/Munazzah1)\ **Post date:** [September 24, 2024, 1:24pm UTC](https://gromacs.bioexcel.eu/t/find-error-while-using-trjconv/10215/9 "2024-09-24T13:24:22Z")
![Screenshot from 2024-09-24 18-48-28](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/34e9c85a721dfe7f42f7d1db2c241bd0ffb88fbe.png) It is not looking well. Due to PBC it has been broken. I am not understand the error. What it is calculated the “The longest distance involved in such interactions is 9.511 nm which is above half the box length.”