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

[Carlos Javier Núñez]

Hi,

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

Regards,
Javier





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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>