# Inconsistent shifts over periodic boundaries in a molecule type consisting of 4 atoms **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [July 3, 2024, 7:27pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-over-periodic-boundaries-in-a-molecule-type-consisting-of-4-atoms/9563 "2024-07-03T19:27:48Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![simran](https://avatars.discourse-cdn.com/v4/letter/s/439d5e/32.png) [@simran](https://gromacs.bioexcel.eu/u/simran)\ **Post date:** [July 3, 2024, 7:27pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-over-periodic-boundaries-in-a-molecule-type-consisting-of-4-atoms/9563/1 "2024-07-03T19:27:48Z")
I am working on a helium water system. I made the topology file using python codes. Using that I generated tpr file but now when i use that tpr file for the energy minimization it show me error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 4 atoms. The longest distance involved in such interactions is 10.075 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. please if any one can help me comment Thank you in advance ---
**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:** [July 4, 2024, 11:46am UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-over-periodic-boundaries-in-a-molecule-type-consisting-of-4-atoms/9563/2 "2024-07-04T11:46:56Z")
We cannot say anything without more information. What kind of bonded interactions are there in your topology? ---
**Author:** ![simran](https://avatars.discourse-cdn.com/v4/letter/s/439d5e/32.png) [@simran](https://gromacs.bioexcel.eu/u/simran)\ **Post date:** [July 4, 2024, 5:18pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-over-periodic-boundaries-in-a-molecule-type-consisting-of-4-atoms/9563/3 "2024-07-04T17:18:54Z")
in my system there is water consisting of 4 atoms - HW1,HW2,OW and MW4: Virtual site or dummy mass used for constraints. and some He atoms that are nonbonded ---
**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:** [July 5, 2024, 9:48am UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-over-periodic-boundaries-in-a-molecule-type-consisting-of-4-atoms/9563/4 "2024-07-05T09:48:22Z")
Then my guess is that you set up your initial coordinates incorrectly, e.g. with some water molecules being split of the periodic boundary before stacking a system. ---
**Author:** ![simran](https://avatars.discourse-cdn.com/v4/letter/s/439d5e/32.png) [@simran](https://gromacs.bioexcel.eu/u/simran)\ **Post date:** [July 5, 2024, 1:54pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-over-periodic-boundaries-in-a-molecule-type-consisting-of-4-atoms/9563/5 "2024-07-05T13:54:26Z")
Yeah I guess, as I have made my topology file using codes. So I’ll check it again. Thank you for the help. ---
**Author:** ![simran](https://avatars.discourse-cdn.com/v4/letter/s/439d5e/32.png) [@simran](https://gromacs.bioexcel.eu/u/simran)\ **Post date:** [July 8, 2024, 5:11pm UTC](https://gromacs.bioexcel.eu/t/inconsistent-shifts-over-periodic-boundaries-in-a-molecule-type-consisting-of-4-atoms/9563/6 "2024-07-08T17:11:55Z")
I examined my toplogy files. I made my itp files for water and run the mdrun for water till nvt and it gave me result. I made the itp file for helium using parmed module and run mdrun till minimization alone for helium it gave me result. However, even though I received a tpr file for minimization when I merged their itp files for combined topology files and used them for mdrun, that tpr file gave me an error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 4 atoms. The longest distance involved in such interactions is 10.075 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. [topol.top](https://gromacs.bioexcel.eu/uploads/short-url/g1IQxv4nrR7LQZfclt2RxedZrxf.top) (169 Bytes) [forcefield\_itp\_file\_and\_Helium\_itp\_file.txt](https://gromacs.bioexcel.eu/uploads/short-url/r4yqmv0LI0QEtROg6cblJWXAR7u.txt) (2.0 KB)