Simply use gmx genconf -nbox 2 2 1 and update the topology to include 4x the number of lipids.

Simply use gmx genconf -nbox 2 2 1 and update the topology to include 4x the number of lipids.

you can use this command in pymol :

"create merge, all"

Thank You very much Justin Lemkul and Masoud Keramati it works now!

However, now I have another problem...

Fatal error:

Atom H1R in residue POPC 314 was not found in rtp entry POPC with 134 atoms

while sorting atoms.

For a hydrogen, this can be a different protonation state, or it

might have had a different number in the PDB file and was rebuilt

(it might for instance have been H3, and we only expected H1 & H2).

Note that hydrogens might have been added to the entry for the N-terminus.

Remove this hydrogen or choose a different protonation state to solve it.

Option -ignh will ignore all hydrogens in the input.

I have not changed anything in the POPC file, so I have no idea why GROMACS gives such an error...

Do You have any suggestions what to do?

The atom names in the coordinate file do not conform to what the force field requires. Lipids generally don't have .hdb entries to construct missing H so -ignh will not be helpful. You need to either correct the atom names yourself or write .hdb entries to use -ignh.

Thank You very much Justin Lemkul ! I will try to correct the atom names by myself.