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

Carlos Javier Núñez carlosjavierna at gmail.com
Mon Oct 8 07:31:23 CEST 2012


visualize your MD trajectory in VMD without water (or solvent) and without
ions (if have).
I hope this helps.


2012/10/6 Albert <mailmd2011 at gmail.com>

> 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.
> thank you very much
> best
> Albert
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