On 8/26/18 12:44 AM, Raag Saluja wrote:
I gave the following commands: gmx_mpi trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center (I first selected 0 and then 1, like in the lysoyme tutorial). gmx_mpi dipoles -f md_noPBC.xtc -s md.tpr Despite that, I am getting opposite values in Mtot and aver. By re-center do you mean something other than that?
Yes, as David said as well, you need to place the center-of-charge (not center-of-mass) at the coordinate origin (not the center of the box) and there is no GROMACS tool that does this. You'll have to code something up yourself.
-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.thelemkullab.com ================================================== -- 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.
