[gmx-users] about box size (III)

[chris.neale at utoronto.ca]

editconf option,-f input.gro -o output.gro -bt triclinic -box 4 4 6
is not recommended for a box size of size is 3,2,6 in x,y,z
use -d 0.0 instead of -box 4 4 6
Read about it here:
http://www.gromacs.org/documentation/reference/online/editconf.html

I am assuming that you are using periodic boundary conditions and  
pressure scaling. In that case -box 4 4 6 will probably be fine, but  
be sure to visualize your system (you could use VMD). If you are  
unsure about periodicity (Tsjerk recently pointed out that what looks  
incorrect may in fact be correct) then I urge you to turn on the  
periodic representation in VMD and look at the system in this manner.

Chris.