# Flat Bottom Position Restraints Insufficient information on Manual **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, restraints\ **Created:** [June 26, 2023, 1:40am UTC](https://gromacs.bioexcel.eu/t/flat-bottom-position-restraints-insufficient-information-on-manual/6682 "2023-06-26T01:40:26Z")\ **Posts on this page:** 1\ **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:** [June 26, 2023, 1:40am UTC](https://gromacs.bioexcel.eu/t/flat-bottom-position-restraints-insufficient-information-on-manual/6682/1 "2023-06-26T01:40:26Z")
GROMACS version: 2021 GROMACS modification: No Hello I’m trying to use flat bottom position restraints to force the formation of a pore in a lipid membrene with the Martini 3.0 coarse grained force field. But I can’t get it to work properly. At first pore formation happened at random, so I wrote a script to delet all lipids in a circle on the membrane creating a whole in the center of the membrane. I tried applying the potential to this system, but then the whole I’d made with the script closes and another one opens right on the edge of the membrane. I needed the pore to be centralized. My restraint setup is as follows: I have these lines on my topol file ```auto ;keep lipid tails out of a cylinder along X Y Z axis to maintain the waterpore: #ifdef VESICLE_LIPIDTAIL_R #ifndef VESICLE_LIPIDTAIL_FC #define VESICLE_LIPIDTAIL_FC 10 #endif [position_restraints] 5 2 8 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 6 2 8 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 7 2 8 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 8 2 8 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 9 2 8 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 10 2 8 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 11 2 8 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 12 2 8 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC #endif ``` and the following line on my mdp file: ```auto define = -DVESICLE_LIPIDTAIL_R=2.00 ``` I’m using a time step of 0.005 instead of the standar of 0.02 for Martini, otherwise the system with the restraints gets to unstable. On the left is the image of the bilayer with the lipids removed with my script, on the right is the bilayer after 1 ns of equilibration. ![bioexcel](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/546d3e125e8e1b3245b864683823e69058a7c679.png) I can’t figure out how to set the coordinates for the potential center, **DVESICLE\_LIPIDTAIL\_R** should be the radius for the potential, but there is no parameter to specify the coordinates for the potential center. All my files can be found in this link: [Google Drive](https://drive.google.com/drive/folders/1P_bCJwwF8BBSkoc3XaTM-L1Xg5rT9_SA?usp=sharing) Thank you