Lipid phosphates moving to membrane hydrophobic core while tails turn to water

GROMACS version: 2022
GROMACS modification: No

I’m trying to simulate a membrane with 12 peptides inserted in a pore,but, whenever I run the energy minimization, all the phosphates migrate to the hydrophobic region of the membrane while the tails turn to water. I first thought this could be a PME problem, related to a system with non zero eletric charge. But grompp doesn’t give me an warning and the calculated net charged based on the topology is zero.

I’m using Slipids for the lipids and Amber ff99sb-ildn for the peptides.

I assembled the peptides in the desired structure using Packmol, and built the membrane with the pore with CHARMM-GUI. I downloaded the itp file for POPC from the Slipids website.

The phosphates are represented in orange and the sodium ions in purple.

my minimization mdp file is as follows:

define          =  -DPOSRES    

integrator      = steep         ; Algorithm (steep = steepest descent minimization)
emtol           = 1        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nmi ;  the minimization converges when the max force is smaller than this value (in units of kJ mol –1 nm –1)
emstep          = 0.01          ; Energy step size
nsteps          = 50000          ; Maximum number of (minimization) steps to perform

cutoff-scheme   = Verlet
ns_type         = grid          ; search neighboring grid cells
nstlist         = 10             ; 50 fs
vdw_modifier    = potential_switch
rcoulomb        = 1.5           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.5           ; short-range van der Waals cutoff (in nm)
rvdw_switch     = 1.4

; Electrostatics
coulombtype	    = PME		; Particle Mesh Ewald for long-range electrostatics
pme_order	    = 4		; cubic interpolation
fourierspacing	= 0.16		; grid spacing for FFT

constraint_algorithm = lincs    ; holonomic constraints
constraints          = all-bonds     ; all bonds (even heavy atom-H bonds) constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy

pbc             =  xyz

I tried doing with and without LINCS and pbc … But no matter what I do I get the same result.

All my files can be found in the this google drive link: for bioexcell - Google Drive

Any help will be appreciated.


Best regards