Thank you. I updated the mdp file. (Is the dihedral defined as a pair of planes rather than a triplet of vectors?) Unfortunately I still get the segmentation fault and similar warnings. I will try to compile the differences between the sample mdp and the one I used, then see which differences I can not understand and then just ask about those.
With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 6 Apr 2020, at 14:44, Justin Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: On 4/6/20 2:33 AM, Marko Petrovic wrote: I figure it might be helpful to see my other files so I include a link: https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin Your dihedral definitions are simply incorrect. pull_coord1_groups = 1 2 2 3 3 4 pull_coord2_groups = 2 3 3 4 4 5 should be pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -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<mailto: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. -- 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.
