# Flat bottomed position restraints not working as intended **URL:** \ **Category:** User discussions\ **Tags:** restraints\ **Created:** [May 28, 2023, 11:07pm UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working-as-intended/6505 "2023-05-28T23:07:28Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![TGaziri](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/tgaziri/32/5191_2.png) [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)\ **Post date:** [May 28, 2023, 11:07pm UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working-as-intended/6505/1 "2023-05-28T23:07:28Z")
GROMACS version: 2021.5 GROMACS modification: No Hello I’m trying to simulate a system with 8 identical peptides and a lipidic membrane, but I want the peptides to interact with only one leaftlet of the membrane. I was told to use Flat-Bottomed position restraints to keep the peptides on one side. But it’s not working as intended, I’ve run a test for 200 ns and the peptides appear kinda locked into place. This isn’t what I want I only want the peptides to be restricted to the upper half of the box. My system can be seem in this picture ![npt](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/341e0219718c4c2c2ee1e75fc07374cef71364a2.png) My topol file can be seen below ```auto #include "./charmm36-jul2022-napht.ff/forcefield.itp" #include "napht-bp100.itp" #ifdef POSRES #include "posre.itp #endif ;;;Flat bottom position restraints [position_restraints] ; i funct g r k 1 2 5 0.5 1000 19 2 5 8.0 1000 20 2 5 8.0 1000 28 2 5 8.0 1000 30 2 5 8.0 1000 32 2 5 8.0 1000 38 2 5 8.0 1000 40 2 5 8.0 1000 42 2 5 8.0 1000 60 2 5 8.0 1000 62 2 5 8.0 1000 64 2 5 8.0 1000 82 2 5 8.0 1000 84 2 5 8.0 1000 86 2 5 8.0 1000 101 2 5 8.0 1000 103 2 5 8.0 1000 105 2 5 8.0 1000 121 2 5 8.0 1000 123 2 5 8.0 1000 125 2 5 8.0 1000 143 2 5 8.0 1000 145 2 5 8.0 1000 147 2 5 8.0 1000 165 2 5 8.0 1000 167 2 5 8.0 1000 169 2 5 8.0 1000 184 2 5 8.0 1000 186 2 5 8.0 1000 188 2 5 8.0 1000 203 2 5 8.0 1000 205 2 5 8.0 1000 207 2 5 8.0 1000 225 2 5 8.0 1000 227 2 5 8.0 1000 229 2 5 8.0 1000 246 2 5 8.0 1000 248 2 5 8.0 1000 #include "popg.itp" ; Include Position restraint file #ifdef POSRES_POPG #include "posre-popg.itp" #endif #include "popc.itp" ; Include Position restraint file #ifdef POSRES_POPC #include "posre-popc.itp" #endif ; Include water topology #include "./charmm36-jul2022.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [position_restraints] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-jul2022.ff/ions.itp" [system] ; Name Protein [molecules] ; Compound #mols Protein 8 POPG 64 POPC 64 SOL 7690 CLA 40 SOD 64 ``` There is not enough information about how to used flat-bottomed postion restraints only, so I used what I could gather from the documentation and posts here on bioexcel. Any help will be appreciated. Thanks ---
**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:** [May 31, 2023, 11:15am UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working-as-intended/6505/2 "2023-05-31T11:15:44Z")
You restraint setup looks correct to me. Could it be that you have set -DPOSRES in your mdp file, which activates the normal position restraints (as well)? ---
**Author:** ![TGaziri](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/tgaziri/32/5191_2.png) [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)\ **Post date:** [June 1, 2023, 10:30pm UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working-as-intended/6505/3 "2023-06-01T22:30:44Z")
Hi, thank you very much for your reply. I just checked my mdp file and I didn’t set -DPOSRES. I’m still unsure what is causing the problem I’m going to try changing the reference positions on the restraints and run it again. Thanks ---
**Author:** ![Elahe](https://avatars.discourse-cdn.com/v4/letter/e/e68b1a/32.png) [@Elahe](https://gromacs.bioexcel.eu/u/Elahe)\ **Post date:** [June 18, 2024, 6:05am UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working-as-intended/6505/4 "2024-06-18T06:05:40Z")
> [@TGaziri](#): > > Hello I’m trying to simulate a system with 8 identical peptides and a lipidic membrane, but I want the peptides to interact with only one leaftlet of the membrane. I was told to use Flat-Bottomed position restraints to keep the peptides on one side. But it’s not working as intended, I’ve run a test for 200 ns and the peptides appear kinda locked into place. This isn’t what I want I only want the peptides to be restricted to the upper half of the box. Dear @TGaziri , I’m trying to simulate a system with a drug and membrane, and I want the drug to interact with only the upper leaflet of the membrane. Can I use the flat bottom position restrain? Did you do it for your system? ---
**Author:** ![TGaziri](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/tgaziri/32/5191_2.png) [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)\ **Post date:** [June 18, 2024, 12:32pm UTC](https://gromacs.bioexcel.eu/t/flat-bottomed-position-restraints-not-working-as-intended/6505/5 "2024-06-18T12:32:23Z")
Hi @Elahe. I put this project on standby, I didn’t do it yet, I believe that you can use flat bottomed potential for your drug.