Thanks Justin. So it is right to run the simulation without ions, then add ions, then re-run with ions with the new topolgy?
Sergio 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: Tuesday, June 20, 2017 4:21:18 PM Subject: Re: [gmx-users] Error running GMX 5.14 On 6/20/17 10:14 AM, Sergio Manzetti wrote: > I run the simulations on the solvated DNA without adding ions. Then at the > end, I added ions to the output tpr of the simulation. At this stage I > waanted then to run the simulaiton with the new tpr. But that does not work. > How did you add ions to a .tpr? This implies adding them to a coordinate file, then adding them to the topology, and correctly compiling a .tpr with grompp. Depending on how you did this, it's likely the cause of your problem. > Is there a tutorial online on how to add Na to DNA with command line? > It's no different than any invocation of genion, which you can get from any tutorial. For instance: gmx genion -s dna_solv.tpr -o dna_solv_ions.gro -p topol.top -pname NA -np 20 -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.
