On 2/7/19 1:36 PM, Mala L Radhakrishnan wrote:
Thanks...but these don't really address the issue I have. I've written my own script now to do re-centering and looping of atoms across the box walls myself, but I am still really unclear why -center does not in fact center the molecule in the box either at its geometric center OR its center of mass (I have written scripts to test both out and neither match, and visually the molecule is clearly not centered in the box) To me it definitely seems like something is not right with this utility or something about the options I've used are conflicting in ways I don't understand: -pbc atom -center (a group from index file) Thanks again for any other ideas...
I've only been loosely following this thread, but I've never had a problem where trjconv didn't center as I wanted. Have you verified that the index group is correct, and you're making the proper selection? What does gmx traj report as the center-of-mass coordinates for those groups before and after trjconv tries to center them?
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.
