[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3
chihying2008 at gmail.com
Sat Jan 2 22:09:24 CET 2010
>From the Gromacs Manual,
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
I visualized the .gro file created by the editconf, the protein is centered
in the box as I can see.
Chih-Ying Lin wrote:
> 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
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
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