Flat Bottom Position Restraints for membrane pore

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GROMACS version: 2023
GROMACS modification: No

Hello

I’m trying to use Flat Bottom Position Restraints to force the formation a single pore in a lipid membrane. The idea was to use the Flat Bottom Position Restraints to keep the lipid tails out of a cylinder in the x axis. I’m using the Martini 3.0 forcefield and a bilayer with 512 lipids per monolayer, but I can’t get it to work, I’ve tried multiple restraints setups, which I extracted from the files charmm-gui uses to equilibrate vesicles for martini (using pores) and removed the lines for restraints in the y and z axis, as those are required for a spherical vesicle, but not a planar membrane and those lines caused artifacts. I’ve run each test run for 100 ns, but only managed to distort the bilayer and form no pore whatsoever.

My files can be acessed in this link Google Drive

I was using a restraint setup as follows

;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    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
      6     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
      7     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
      8     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
      9     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
     10     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
     11     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
     12     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
#endif

;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    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
      6     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
      7     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
      8     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
      9     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
     10     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
     11     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
     12     2    6   -VESICLE_LIPIDTAIL_R  VESICLE_LIPIDTAIL_FC
#endif

in my .mdp file I’ve added the following line:

define                   = -DVESICLE_LIPIDTAIL_R=5.00

The restraint lines are duplicated because I used a mixed POPC:POPG bilayer and had to define the restraints for both lipid types.

From what I’ve tried the distance from the center at which the potential is applied, given by the VESICLE_LIPIDTAIL_FC variable, must be 10 at most, or the system simply crashes.
I’ve tried multiple VESICLE_LIPIDTAIL_R values but none have worked

Any help will be highly appreciated