Thanks, this worked. 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: "Mark Abraham" <mark.j.abra...@gmail.com> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Tuesday, June 20, 2017 5:04:24 PM Subject: Re: [gmx-users] Error running GMX 5.14 Hi, # make initial gro and .top somehow gmx grompp -f whatever -c initial -p initial -o for-genion cp initial.top with-ions.top gmx genion -f for-genion -p with-ions.top -o with-ions gmx grompp -f em -p with-ions -c with-ions -o ready-for-em gmx mdrun -s ready-for-em Mark On Tue, Jun 20, 2017 at 4:45 PM Sergio Manzetti < sergio.manze...@fjordforsk.no> wrote: > Precisely. 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 <+47%2057%2069%2056%2021> > [ 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 4:42:37 PM > Subject: Re: [gmx-users] Error running GMX 5.14 > > On 6/20/17 10:36 AM, Sergio Manzetti wrote: > > One simple question, where does one get the sytem input for genion, as > it only want tpr, unless one uses grompp? > > > > Yes, you have to use grompp on the solvated system to get a .tpr of the > system > that contains no ions. You pass that .tpr to genion and then never use it > again. > > -Justin > > > > > 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 <+47%2057%2069%2056%2021> > > [ 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 4:39:03 PM > > Subject: Re: [gmx-users] Error running GMX 5.14 > > > > On 6/20/17 10:32 AM, Sergio Manzetti wrote: > >> Let me see if I have it right. > >> > >> After doing the minimization of the system without ions, I add ions to > the minimized system and replace the waters. > >> > > > > I see no point in doing multiple rounds of minimization like this. Just > build > > the whole system and minimize. > > > >> Then I use grompp to set up the sim with the output tpr from the genion > command as -c file, and the original topology ? > >> > > > > No. The .tpr file provided to genion is never used again. It has one > purpose > > only and it is not an output from genion at all. > > > > This is all very basic stuff. Please try some tutorials: > > > > http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use > > > > -Justin > > > >> 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 <+47%2057%2069%2056%2021> > >> [ 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. -- 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.