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

[gromacs query]

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