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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
