Dear gromacs users, I am working on a martini cg model of a mixed bilayer system. However I am a bit confused about choosing the correct box length using editconf. If I use gmx editconf -c -d 1.0 i.e. keeping 1 nm distance between the bilayer and the box, then the resulting box size is very large. Generally for proteins we follow this protocol of choosing a box length where the protein atoms are at least 1 nm away from the box edge i.e their mirror images are ~2 nm apart from each other. Should I follow a similar protocol for choosing the box length for lipid bilayers as well or something else can also be employed? For example, I have been using charmm-gui for lipid bilayer generation, there I have seen that the packed lipid molecules in the xy-plane are situated very close to the edge of the box. In that case won’t that result in some unrealistic interactions between those lipid molecules at the edge and their images?
Any help will be much appreciated.