[gmx-users] Centering the molecule
mark.j.abraham at gmail.com
Mon Jun 4 14:51:26 CEST 2018
Trjconv -pbc mol is documented to do a particular thing.
If that's not what you want, even though it may have coincidentally done
what you wanted on some other trajectory, then please reconsider that
If it's not doing what it says, it would be good to see some more detail
than "it doesn't work how I expected."
On Mon, Jun 4, 2018, 10:32 <spss4 at iacs.res.in> wrote:
> Hi all
> I want to center my molecule into a rectangular box by GROMACS. I am using
> the following command:
> gmx trjconv -f traj.trr -s md.tpr -center -pbc mol -b 100 -e 120 -o
> But output shown is still out of the box. This command works for cubic
> box. Is there anything different flag for rectangular box? My box size is
> 5 5 7.
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