[gmx-users] Question regarding rebuilding the simulation box

[ali.khourshaei71 at student.sharif.edu]

Dear gromacs user, 

I have 2 question regarding the building of the simulation box from an
initial configuration. 

1. I have a rectangular box ( 6.45 * 5.35 * 7 ). How can I build a new
simulation box, containing these atom but in a cubic manner ( 7 * 7 * 7
) 

2. If I delete some water molecules from an initial configuration by
omitting these molecules manually from the .gro file, is this valid ? 

Sincerely, 

Ali