[gmx-users] regarding pbc issue

Justin Lemkul jalemkul at vt.edu
Sat Jan 13 14:55:22 CET 2018

On 1/13/18 7:53 AM, Vidya R wrote:
> 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.

Run both and see if there is a difference. gmx rdf should be PBC-aware, 
so you should get the same result.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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