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

gromacs query gromacsquery at gmail.com
Mon May 6 10:21:06 CEST 2013

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

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?


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