[gmx-users] regarding pbc issue

[Vidya R]

Hi gmx users,

I used the following commands after simulation run (organic compound in
water, to calculate rdf)



 gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
 gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc


To use the following command, which xtc file should I use?

gmx rdf -f ---.xtc -n index.ndx

*prd or newtraj.xtc?*

Please clear my doubt.

Thanks,

*Vidya.R*