Maybe someone can suggest a method to add ions to the system without that they appear as water molecules?
The em looks like this: define = integrator = steep emtol = 100.0 emstep = 0.0001 nsteps = 10000 ; output frequency nstxout = 50 nstvout = 0 nstfout = 0 nstlog = 50 nstenergy = 50 nstxtcout = 0 xtc_grps = system ; nstlist = 10 pbc = xyz rlist = 1.4 cutoff-scheme = group coulombtype = PME rcoulomb = 1.4 vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; constraints = none constraint_algorithm = LINCS implicit_solvent = no E_x = E_y = E_z = 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 ] From: "Smith, Micholas D." <[email protected]> To: "gmx-users" <[email protected]> Sent: Tuesday, June 20, 2017 2:09:08 PM Subject: Re: [gmx-users] Error running GMX 5.14 What does your *.mdp file look like? Its hard to judge what the next step should be from what you've given so far. -Micholas =================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: [email protected] <[email protected]> on behalf of Sergio Manzetti <[email protected]> Sent: Tuesday, June 20, 2017 7:48 AM To: [email protected] Subject: [gmx-users] Error running GMX 5.14 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. 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 [email protected]. -- 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 [email protected]. -- 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 [email protected].
