[gmx-users] trjconv -pbc atom -center rect

XAvier Periole x.periole at rug.nl
Fri Jun 19 09:02:33 CEST 2009

did you try the option -nojump in trjconv ?

On Jun 19, 2009, at 3:56 AM, Chih-Ying Lin wrote:

> Hi
> I have a protein+several ligand in the simulation box.
> After 5ns, the protein drift to the right edge of the box and the
> ligand drift to the left edge of the box.
> with this command =>
> trjconv -pbc atom -center rect
> the most part of the protein is still in the right edge of the box
> the small part of the protein is shifted in the left edge of the box
> and i can clearly see that the ligand attach onto the protein.
> but, the protein is NOT in the center of the box ???
> so, how can i use trjconv command to center protein and to see the
> ligand attaching on the protein?
> Thank you
> Lin
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