# Flat-bottomed position restraints not working **URL:** \ **Category:** User discussions\ **Created:** [February 8, 2021, 7:19am UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working/1554 "2021-02-08T07:19:58Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![gonzaloqe](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/gonzaloqe/32/653_2.png) [@gonzaloqe](https://gromacs.bioexcel.eu/u/gonzaloqe)\ **Post date:** [February 8, 2021, 7:19am UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working/1554/1 "2021-02-08T07:19:58Z")
GROMACS version:2020.3 GROMACS modification: No Dear GROMACS users, I had try to do osmotic pressure for NH4+ Cl- molecules in a water solution simulation using a flat-bottomed position restraints as other works in literature. I copy the itp that I use for the molecules of NH4+: [moleculetype] ; Name nrexcl NH4 3 [atoms] ; nr type resnr resid atom cgnr charge mass 1 N3 1 NH4 NP 1 -0.400000 14.0067 2 H 1 NH4 H 1 +0.350000 1.0080 3 H 1 NH4 H 1 +0.350000 1.0080 4 H 1 NH4 H 1 +0.350000 1.0080 5 H 1 NH4 H 1 +0.350000 1.0080 ;total charge +1.000 [bonds] ; ai aj funct c0 c1 1 2 1 ; N3 H 1 3 1 ; N3 H 1 4 1 ; N3 H 1 5 1 ; N3 H [angles] ; ai aj ak funct angle fc 2 1 3 1 2 1 4 1 2 1 5 1 3 1 4 1 3 1 5 1 4 1 5 1 [position\_restraints] ; atom type g r (nm) K (kJ/mol/nm2) 1 2 5 3.0 1000 2 2 5 3.0 1000 3 2 5 3.0 1000 4 2 5 3.0 1000 5 2 5 3.0 1000 The objetive for me is to have all the NH4+ molecules within a cutoff in the Z direction of 3 nm from the center of the box, where the lenght Lz is 8 nm. But when i run the simulations in NVT is seems that every molecule of NH4+ is moving in all z directions as the restriction are not applied. The itp for the molecule is correct or something else? kind regards ---
**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:** [February 8, 2021, 9:38am UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working/1554/2 "2021-02-08T09:38:23Z")
Did you supply a restraint file to grompp with the -r option with all z-coordinates set to 4? ---
**Author:** ![gonzaloqe](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/gonzaloqe/32/653_2.png) [@gonzaloqe](https://gromacs.bioexcel.eu/u/gonzaloqe)\ **Post date:** [February 8, 2021, 7:09pm UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working/1554/3 "2021-02-08T19:09:09Z")
I used the same configuration file in the -c option as in the -r option. Could you explain how to set the z coordinates? Best regards. ---
**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:** [February 8, 2021, 7:50pm UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working/1554/4 "2021-02-08T19:50:28Z")
Change the coordinates using a text editor, or write a script to do so. ---
**Author:** ![gonzaloqe](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/gonzaloqe/32/653_2.png) [@gonzaloqe](https://gromacs.bioexcel.eu/u/gonzaloqe)\ **Post date:** [February 9, 2021, 2:57pm UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working/1554/5 "2021-02-09T14:57:56Z")
It worked. thanks Justin and Hess. Kind regards.