What is the reason for warning the atom name?

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1

GROMACS version:2021
GROMACS modification: Yes/No
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I get the following error during ionization complex of membrane and nanoparticles. However, if I use only from the membrane, I not get this warning. Why does the addition of nanoparticles cause this problem?

warning
warning775×624 83.4 KB

start
start895×641 15.5 KB

end
end571×660 11.2 KB

2

Look at the [ molecules ] section in your .top. It reads:

DPPC 1
LIG 1
REC 1
…

What grompp expects is that your structure (.pdb/.gro) will first contain all atoms for one DPPC molecule, then all atoms for the LIG molecule, then all atoms from the REC molecule… And so on, exactly in the order and quantity specified in molecule definitions in .top/.itp files. The error indicates that DPPC either isn’t the first molecule in your structure (and hence the matching is lost for the next 16190 atoms).

Best,
Miłosz