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.manze...@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 > 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: 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" <jalem...@vt.edu> > > To: "gmx-users" <gmx-us...@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 > > 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? 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