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

Chih-Ying Lin chihying2008 at gmail.com
Sat Jan 2 22:09:24 CET 2010

>From the Gromacs Manual,
editconf =>
The box can be modified with options -box, -d and -angles. Both -box
and -dwill center the system in the box.

so, without -c option, the protein is already centered in the box.
and, there is no description in the manual that people cannot use -d and
-box simultaneously.

I visualized the .gro file created by the editconf,  the protein is centered
in the box as I can see.

Thank you

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.  You cannot
use -d
and -box simultaneously.  They are mutually exclusive.  You are also not
centering the protein in the box (you are not using the -c option).  So, in
fact, what you're doing was exactly what my problem was - not centering and
potentially defining the box incorrectly.
I would suggest that you at least try rebuilding your system, because the
command is certainly wrong.
> Thank you
> Lin
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