[gmx-users] Centering the molecule

Mark Abraham 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
> test.gro
> 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.
> Thanks
> Sunipa
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