# Flat-bottom potential renders an unstable system **URL:** \ **Category:** User discussions\ **Tags:** forcefield, mdp-parameters, mdrun\ **Created:** [August 3, 2023, 2:04pm UTC](https://gromacs.bioexcel.eu/t/flat-bottom-potential-renders-an-unstable-system/6960 "2023-08-03T14:04:54Z")\ **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:** [August 3, 2023, 2:04pm UTC](https://gromacs.bioexcel.eu/t/flat-bottom-potential-renders-an-unstable-system/6960/1 "2023-08-03T14:04:54Z")
GROMACS version: 2022 GROMACS modification: No I’m trying to equilibrate a membrane generated with CHARMM-GUI for the Martini forcefield. My membrane contains 512 lipids per monolayer and I’m using 28000 water beads (equivalent to 110 waters per lipid), this membrane as pre-equilibrated using CHARMM-GUI’s protocol. I want to make a pore in the membrane using the Flat-Bottom potential to keep the lipid tails out of a region on the z-axis. I’m following the CHARMM-GUI’s protocol for equilibrating vesicles, but when I apply the potential, the system symply crashes, most of the time `mdrun` just freezes and refuses to run. It won’t even give any error except sometimes a `segmentatium fault` I have the following lines in my itp file under the lipids definition: ```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 5 #endif [position_restraints] 5 2 2 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 6 2 2 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 7 2 2 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 8 2 2 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 9 2 2 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 10 2 2 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 11 2 2 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC 12 2 2 -VESICLE_LIPIDTAIL_R VESICLE_LIPIDTAIL_FC #endif ``` and my mdp file is as follows: ```auto define = -DVESICLE_LIPIDTAIL_R=2.00 integrator = md tinit = 0.0 dt = 0.002 nsteps = 1000000 nstlog = 1000 nstenergy = 1000 nstxout-compressed = 1000 compressed-x-precision = 100 cutoff-scheme = Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 epsilon_r = 15 coulombtype = reaction-field rcoulomb = 1.1 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 tcoupl = v-rescale tc-grps = membrane solute tau_t = 1.0 1.0 ref_t = 303.15 303.15 ; Pressure coupling: Pcoupl = berendsen Pcoupltype = semi-isotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN: gen_vel = yes gen_temp = 303.15 gen_seed = 8415458562 refcoord_scaling = all ``` If I decreade the ` -DVESICLE_LIPIDTAIL_R` value to 0.50 or lower the simulation runs, but it won’t produce the desired effect. Any value of `#define VESICLE_LIPIDTAIL_FC ` greater than 5 also makes the simulation crash How can I avoid the system crashing?? I thought perhaps my system is too small, but a bilayer with 512 lipids per monolayer is already pretty big. So I’m clueless on how to make this work Thanks