Hi Justin, the sequence was: gmx editconf ....
gmx solvate .... gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA -nname CL then: gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o dna_solv_NaCl_EM gmx mdrun This worked. Then for the sim: dna_solv_NaCl_EM.gro does not contain any ions. 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: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Wednesday, June 21, 2017 4:44:16 PM Subject: Re: [gmx-users] Genion On 6/21/17 10:30 AM, Sergio Manzetti wrote: > Hello, genion worked, and grompp was used to run the output conf from genion. > Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no > longer contains the Na Cl ions added to the system. When setting up the > simulation, the input confout.gro has no Na Cl ions, and the procedure is > therefore not working. > > Why is this so? Does one have to do the genion procedure each time one wants > to use gromp with a new mdp file? > You run genion once to add ions to your system. Please provide the exact sequence of commands you're using. It's very hard to follow what you're describing. mdrun cannot delete anything, so "no longer contains the Na Cl ions" is impossible. Either the ions are there in the beginning or they're not. If you're using mdrun to run the .tpr file you're sending to genion, don't. There's no point. That .tpr file is not for a simulation, it's just for genion. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
