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

Justin Lemkul jalemkul at vt.edu
Mon May 6 12:07:42 CEST 2013

On 5/6/13 4:21 AM, gromacs query 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)

What you are seeing is a completely normal consequence of periodic boundary 
conditions.  You don't need to change the trajectory in any way to do density 
measurements; the resulting values will be the same before and after centering, 
since there is no "outside" or "center" of an infinite system.


> 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


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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