Replicating lipid bilayer

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I have centered a large protein inside a dppc128 lipid bilayer. Then as given in Justin tutorial on membrane simulation, I used following commands,

gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p -r system_inflated.gro -o system_inflated_em.tpr

gmx mdrun -deffnm system_inflated_em

I got warning messages showing ligang 1,4 interactions and the force didnt converge. It showing many overlapping atoms.

How can I overcome this ?

I tried increasing the nmbr of steps and tried to correct the coordinates of atoms in .gro file, but it has many such atoms.

Also, I ttried to increase the lipid bilayer from 128 to 256 so as to avoid the clash, I used gmx genconf -nbox 2 1 1 when I got 2 separate membrane patches but how to merge them to one (screenshot attached). or should I use any other lipid ?

Am really stuck as to how to overcome this issue…Kindly help

I am from a pure chemistry background and hence find it v. difficult.