[gmx-users] Re: correct traj for water/ions density

[gromacs query]

Sorry forgot to add:::

by doing this I can see my polymer near the center of box


On Mon, May 6, 2013 at 11:21 AM, gromacs query <gromacsquery at gmail.com>wrote:

> Dear All,
>
> I want to calculate water and ions density around polymer. After MD I see
> my polymer goes near the edges of box and rather some part is out of box.
> So in order to calculate water and ion density I think polymer should be
> near the center of box (please correct me if wrong)
>
> So by doing this:
>
> trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc
> mol -center
>
> Select group for centering: I selected my polymer only
> Select group for output: I selected all atoms (polymer + water + ions)
>
> Please let me know is this correct way of modifying trajectory to
> calculate water and ion density?
>
> regards,
> Jiom
>