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

gromacs query gromacsquery at gmail.com
Mon May 6 10:23:47 CEST 2013

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

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