[gmx-users] Error running GMX 5.14

[Mark Abraham]

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.manzetti at 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" <jalemkul at vt.edu>
> To: "gmx-users" <gmx-users at 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" <jalemkul at vt.edu>
> > To: "gmx-users" <gmx-users at 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" <jalemkul at vt.edu>
> >> To: "gmx-users" <gmx-users at 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
>
> jalemkul at 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-request at 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-request at gromacs.org.