[gmx-users] Genion

Thu Jun 22 14:30:08 CEST 2017

Hi,

The error message has a helpful URL that'll take you to the same advice
that we give several times a week on here :-)

Mark

On Thu, 22 Jun 2017 14:27 Sergio Manzetti <sergio.manzetti at fjordforsk.no>
wrote:

> Thanks, Worked out. Now I got a note saying:
>
> NOTE 1 [file em.mdp]:
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be
> removed in a future release when all interaction forms are supported for
> the verlet scheme. The verlet scheme already scales better, and it is
> compatible with GPUs and other accelerators.
>
>
>
> Fatal error:
> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> How can I fix the system, when the energy minimization step cannot?
>
>
> Sergio
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
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>
>
>
> From: "Justin Lemkul" <jalemkul at vt.edu>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Thursday, June 22, 2017 2:21:17 PM
> Subject: Re: [gmx-users] Genion
>
> On 6/22/17 8:14 AM, Sergio Manzetti wrote:
> > OK, now I treied writing Na Cl and not NA and CL and get:
> >
>
> This is what you did before, so naturally you get the same thing.
>
> > Na)
> > Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >
>
> As I said, using mixed case is incorrect. The [moleculetype] entries in
> ions.itp expect all caps. Use all caps.
>
> -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
> > [ 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: Thursday, June 22, 2017 2:09:02 PM
> > Subject: Re: [gmx-users] Genion
> >
> > On 6/22/17 7:30 AM, Sergio Manzetti wrote:
> >> Hi, the procedure as defined by Juistin worked out well. However, a new
> problem has occurred. At mdrun for the minimization, I get:
> >>
> >> -------------------------------------------------------
> >> Program gmx mdrun, VERSION 5.1.2
> >> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp,
> line: 276
> >>
> >> Fatal error:
> >> 1 particles communicated to PME rank 3 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> >> This usually means that your system is not well equilibrated.
> >> For more information and tips for troubleshooting, please check the
> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >>
> >>
> >> This may be caused by the solvent replacement of genion by Na Cl:
> >>
> >>
> >>
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
> >> Will try to add 130 Na ions and 90 Cl ions.
> >> Select a continuous group of solvent molecules
> >> Group 0 ( System) has 98254 elements
> >> Group 1 ( DNA) has 1333 elements
> >> Group 2 ( Water) has 96921 elements
> >> Group 3 ( SOL) has 96921 elements
> >> Group 4 ( non-Water) has 1333 elements
> >> Select a group: 3
> >> Selected 3: 'SOL'
> >> Number of (3-atomic) solvent molecules: 32307
> >> Replacing solvent molecule 3244 (atom 11065) with Na
> >> Replacing solvent molecule 8993 (atom 28312) with Na
> >> Replacing solvent molecule 7088 (atom 22597) with Na
> >> Replacing solvent molecule 29442 (atom 89659) with Na
> >> Replacing solvent molecule 30079 (atom 91570) with Na
> >> Replacing solvent molecule 5128 (atom 16717) with Na
> >> Replacing solvent molecule 10705 (atom 33448) with Na
> >> Replacing solvent molecule 1418 (atom 5587) with Na
> >> Replacing solvent molecule 6608 (atom 21157) with Na
> >> Replacing solvent molecule 28124 (atom 85705) with Na
> >> Replacing solvent molecule 5440 (atom 17653) with Na
> >> Replacing solvent molecule 31518 (atom 95887) with Na
> >> Replacing solvent molecule 16384 (atom 50485) with Na
> >> Replacing solvent molecule 17675 (atom 54358) with Na
> >> Replacing solvent molecule 23446 (atom 71671) with Na
> >> Replacing solvent molecule 15659 (atom 48310) with Na
> >> Replacing solvent molecule 18442 (atom 56659) with Na
> >> Replacing solvent molecule 23777 (atom 72664) with Na
> >> Replacing solvent molecule 5965 (atom 19228) with Na
> >> Replacing solvent molecule 15375 (atom 47458) with Na
> >> Replacing solvent molecule 30985 (atom 94288) with Na
> >> Replacing solvent molecule 19076 (atom 58561) with Na
> >> Replacing solvent molecule 18065 (atom 55528) with Na
> >> Replacing solvent molecule 22711 (atom 69466) with Na
> >> Replacing solvent molecule 27097 (atom 82624) with Na
> >> Replacing solvent molecule 21561 (atom 66016) with Na
> >> Replacing solvent molecule 18592 (atom 57109) with Na
> >> Replacing solvent molecule 22174 (atom 67855) with Na
> >> Replacing solvent molecule 17888 (atom 54997) with Na
> >> Replacing solvent molecule 13005 (atom 40348) with Na
> >> Replacing solvent molecule 3481 (atom 11776) with Na
> >> Replacing solvent molecule 22603 (atom 69142) with Na
> >> Replacing solvent molecule 9899 (atom 31030) with Na
> >> Replacing solvent molecule 3438 (atom 11647) with Na
> >> Replacing solvent molecule 12180 (atom 37873) with Na
> >> Replacing solvent molecule 32219 (atom 97990) with Na
> >> Replacing solvent molecule 23159 (atom 70810) with Na
> >> Replacing solvent molecule 27929 (atom 85120) with Na....
> >>
> >>
> >> which then reflects on grompp as:
> >>
> >>
> >>
> >> Setting the LD random seed to 3274024379
> >> Generated 2211 of the 2211 non-bonded parameter combinations
> >> Generating 1-4 interactions: fudge = 0.5
> >> Generated 2211 of the 2211 1-4 parameter combinations
> >> Excluding 3 bonded neighbours molecule type 'DNA_chain_E'
> >> Excluding 3 bonded neighbours molecule type 'DNA_chain_F'
> >> Excluding 2 bonded neighbours molecule type 'SOL'
> >> Excluding 1 bonded neighbours molecule type 'NA'
> >> Excluding 1 bonded neighbours molecule type 'CL'
> >> Warning: atom name 97595 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97596 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97597 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97598 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97599 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97600 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97601 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97602 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97603 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97604 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97605 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97606 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97607 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97608 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97609 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97610 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97611 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97612 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97613 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> Warning: atom name 97614 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >> (more than 20 non-matching atom names)
> >>
> >> WARNING 1 [file topol.top, line 50]:
> >> 220 non-matching atom names
> >> atom names from topol.top will be used
> >> atom names from dna_solv_NaCl.gro will be ignored
> >>
> >>
> >>
> >>
> >>
> >> Giving the mdrun problem..
> >>
> >>
> >> Not sure how to get by this!
> >>
> >
> > The mismatching names are not causing the failure. You're getting what
> you
> > asked for as you requested "Na" and "Cl" ions be added. This does not
> match the
> > convention in ions.itp, which uses "NA" and "CL" for ions (this is a
> standard
> > GROMACS thing - elemental symbols in all caps should always be used for
> -pname
> > and -nname). But sodium is still sodium and chloride is still chloride,
> so your
> > topology is not actually out of step with the coordinates.
> >
> > Your initial configuration is simply so you did not adequately minimize
> or
> > equilibrate prior to running dynamics, as the mdrun error suggests.
> >
> > -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
>
> ==================================================
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