editconf -f in.gro -o out.gro -d 0.0 -bt cubic ---original message--- hi everyone my system contain 2 monolayers,and it is more then 6nm in the z direction,and my box is 3.000,3.000,3.000, so it always wrong when mdrun,it said the box only this size,i want to know how to resolve my quetion ? thanks!