[gmx-users] how to center to molecule in pbc box?

Justin Lemkul jalemkul at vt.edu
Sat Oct 6 11:58:32 CEST 2012

On 10/6/12 4:08 AM, Albert wrote:
> hello:
> I am using the following command for md production in gromacs:
> grompp -f md.mdp -p md.top -o md.tpr
> mpirun -np 64 mdrun -s md.tpr -x md.xtc -g md.log
> However, I found that the md.xtc file need command:
> trjconv -f md.xtc -o convert.xtc -pbc mol
> to put the molecule in the centre of pbc box, otherwise it is messy when we
> visualize in VMD. I am wondering, is it possible to ask mdrun generate the .xtc
> file cetering the molecule in PBC box automatically and we no longer need to use
> trjconv command to convert it.

No, it is not.  A periodic system has no center, and the centering algorithm is 
merely a convenience for visualization.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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