Hi, I have a system with DNA and water, and given the charge of the DNA of -20, genion was used to add +20 charge to the gro file. The energy minimization step gives then a warning:
WARNING 2 [file em.mdp]: The sum of the two largest charge group radii (16.704304) is larger than rlist (1.200000) Which is the ignored using maxwarn option. When getting to the em step: Fatal error: step 25: Water molecule starting at atom 31535 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. However, these are not waters, but there are sodium ions added to the system by replacing 20 water molecules, which grompp thinks are waters. The index file does not contain info about these, as also there, the Sodium are not identified and differentiated from water molecules. What is the best approach here to correct this? Thanks! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] -- 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.
