[gmx-users] Error running GMX 5.14
Sergio Manzetti
sergio.manzetti at fjordforsk.no
Tue Jun 20 16:19:11 CEST 2017
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.
Is there a tutorial online on how to add Na to DNA with command line?
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
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From: "Mark Abraham" <mark.j.abraham at gmail.com>
To: "gmx-users" <gmx-users at gromacs.org>
Sent: Tuesday, June 20, 2017 3:09:31 PM
Subject: Re: [gmx-users] Error running GMX 5.14
Hi,
On Tue, Jun 20, 2017 at 2:41 PM Sergio Manzetti <
sergio.manzetti at fjordforsk.no> wrote:
> I can add ions to the final system, after having simulated it without
> ions. But what would the point be?
> This is the strange thing, genion treats only tpr files, and not gro files
> with solvated states
>
The simplest explanation for your observations is that you are running
genion to get the new coordinate file, and then using it with a topology
that does not match (obviously the same .top file that generated the .tpr
you gave to grompp before genion will not match the gro generated by
genion, because it now needs to describe those ions, and fewer solvent
molecules), *and* ignoring when grompp complained that the atom names don't
match. But we have to guess because you haven't shared how you are running
all the tools in your workflow. Your .mdp files are not at all relevant.
Mark
> 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 2:29:36 PM
> Subject: Re: [gmx-users] Error running GMX 5.14
>
> On 6/20/17 8:22 AM, Sergio Manzetti wrote:
> > Maybe someone can suggest a method to add ions to the system without
> that they appear as water molecules?
> >
>
> The job of genion is to replace water molecules with ions. There is no way
> that
> grompp can turn one into the other; you would get a fatal error about
> mismatching names and/or numbers of atoms in the case of a flawed
> topology. I
> suggest you verify the contents of your topology (which should have been
> automatically updated by genion to be correct) and any output from grompp
> to
> make sure you're not ignoring any additional problems. Then check that your
> interpretation of atom numbers is correct. I find it extremely unlikely
> that
> mdrun is complaining about trying to SETTLE an ion (it's topologically
> impossible).
>
> -Justin
>
> > 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 <+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: "Smith, Micholas D." <smithmd at ornl.gov>
> > To: "gmx-users" <gmx-users at gromacs.org>
> > 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: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sergio
> Manzetti <sergio.manzetti at fjordforsk.no>
> > Sent: Tuesday, June 20, 2017 7:48 AM
> > To: gmx-users at gromacs.org
> > 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 <+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 ]
> >
>
> --
> ==================================================
>
> 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
>
> ==================================================
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