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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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