[gmx-users] Re: Simulation Box break into 16 domains => Gromacs 3.3.3

Chih-Ying Lin wrote: Hi From the Gromacs Manual, http://manual.gromacs.org/current/online/editconf.html editconf => The box can be modified with options -box, -d and -angles. Both -box and -d will center the system in the box. so, without -c option, the protein is already centered in the

[gmx-users] Re: Simulation Box break into 16 domains => Gromacs 3.3.3

Chih-Ying Lin wrote: Hi As I posted the command list earlier, to create the box editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box 6.0 6.0 6.0 So, I think Justin's case is not the same as mine. Mark already pointed out that your command line is malformed. Yo