GROMACS modification: No
I have a bilayer of thylakoid comprising of four different lipids and water. I am using coarse-grained martini force field.
While using commands :-
gmx grompp -f ions.mdp -c complete_bilayer_newbox.gro -p single_plant.top -o ions.tpr -maxwarn 2
gmx genion -s ions.tpr -o complete_bilayer_newbox_ions.gro -p single_plant.top -pname NA -nname CL -neutral
Due to this water particle are segregating into oneside and other lipids are missing up resulting in complete destruction of bilayer. This really seems odd, since before I have never encountered such type of error.
You’re adding atomistic ions to a CG system? Doesn’t MARTINI have its own ion particles that you should be using instead?
This shouldn’t happen unless you chose “System” for replacement by ions. But I’d emphasize my point above, I don’t think you want to be adding ions like this at all.
Yes martini has its own ions particles. And I am using that. I think my error cam because i missed or neglected the warning that gromacs was giving. Gromacs was not able to identify some atoms and hence it was replacing it with some other atoms. As a result it was messing with the bilayer. I have corrected it and now it seems good.
But now I am facing the error - “No more replaceable solvent!”
Any comments on that. Because I think there are sufficient amount of water present (i.e.3081 in single leaflet) and ions needed to neutralise the bilayer is 144.
This error is solved by using the index file.