Dear Justin Lemkul, I have looked at the log file as below.
Initializing Domain Decomposition on 16 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.668 nm, Tab. Bonds, atoms 1277 1278 multi-body bonded interactions: 1.460 nm, Tab. Dih., atoms 1226 1229 Minimum cell size due to bonded interactions: 1.500 nm Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 16 cells with a minimum initial size of 1.875 nm The maximum allowed number of cells is: X 3 Y 3 Z 3 Does this mean that I need to use "-dds 1.25" mdrun option? Thank you. Best regards, Changwoon Jang On Fri, Jul 22, 2016 at 7:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/22/16 7:03 PM, Chang Woon Jang wrote: > >> Dear Justin A. Lumkul, >> >> Thank you for your answer. I am sorry for asking what is DD. My >> topology >> topol.top file is below. Would you please tell me about what is DD? How >> can >> I set up in topology file? >> >> > DD = domain decomposition. Please look in the .log file for how it is > being set up and provide that information if you need help troubleshooting > it. Also use Google; this error comes up (and gets solved) every couple of > days. > > -Justin > > > Thank you. >> >> Best regards, >> Changwoon Jang >> >> >> >> [ defaults ] >> >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> >> 1 1 no 0.0 0.0 >> >> >> [ atomtypes ] >> >> ;type mass charge ptype sigma epsilon >> >> A 75.087799 0.000 A 1.000000000 1.000000000 >> >> B 76.097998 0.000 A 1.000000000 1.000000000 >> >> C 42.080999 0.000 A 1.000000000 1.000000000 >> >> D 74.103099 0.000 A 1.000000000 1.000000000 >> >> E 99.153398 0.000 A 1.000000000 1.000000000 >> >> F 116.160799 0.000 A 1.000000000 1.000000000 >> >> G 58.080399 0.000 A 1.000000000 1.000000000 >> >> >> [ moleculetype ] >> >> DGA 3 >> >> >> [atoms] >> >> ; nr type resnr residue atom cgnr charge mass >> >> 1 A 1 DGA A1 1 0.000000 75.087799 >> >> 2 B 1 DGA B1 2 0.000000 76.097998 >> >> 3 C 1 DGA C 3 0.000000 42.080999 >> >> 4 B 1 DGA B2 4 0.000000 76.097998 >> >> 5 A 1 DGA A2 5 0.000000 75.087799 >> >> >> >> [ bonds ] >> >> 1 2 8 1 1.0 ; 1:bond:1 >> >> 2 3 8 1 1.0 ; 1:bond:2 >> >> 3 4 8 1 1.0 ; 1:bond:3 >> >> 4 5 8 1 1.0 ; 1:bond:4 >> >> >> [ angles ] >> >> 1 2 3 8 1 1.0 ; 1:angle:1 >> >> 2 3 4 8 1 1.0 ; 1:angle:2 >> >> 3 4 5 8 1 1.0 ; 1:angle:3 >> >> >> [ dihedrals ] >> >> 1 2 3 4 8 1 1.0 ; 1:ABCBdihedral:1 >> >> 2 3 4 5 8 1 1.0 ; 1:ABCBdihedral:2 >> >> >> [ moleculetype ] >> >> J400 3 >> >> >> [atoms] >> >> ; nr type resnr residue atom cgnr charge mass >> >> 1 D 1 J400 D1 1 0.000000 74.103099 >> >> 2 E 1 J400 E1 2 0.000000 99.153398 >> >> 3 F 1 J400 F1 3 0.000000 116.160799 >> >> 4 G 1 J400 G1 4 0.000000 58.080399 >> >> 5 D 1 J400 D2 5 0.000000 74.103099 >> >> >> [ bonds ] >> >> 1 2 8 1 1.0 ; 1:bond:1 >> >> 2 3 8 1 1.0 ; 1:bond:2 >> >> 3 4 8 1 1.0 ; 1:bond:3 >> >> 4 5 8 1 1.0 ; 1:bond:4 >> >> >> [ angles ] >> >> 1 2 3 8 1 1.0 ; 1:angle:1 >> >> 2 3 4 8 1 1.0 ; 1:angle:2 >> >> 3 4 5 8 1 1.0 ; 1:angle:3 >> >> >> [ dihedrals ] >> >> 1 2 3 4 8 1 1.0 ; 1:dihedral:1 >> >> 2 3 4 5 8 1 1.0 ; 1:dihedral:2 >> >> >> [ system ] >> >> ; Name >> >> Built with Packmol >> >> >> [ molecules ] >> >> ; Compound #mols >> >> DGA 200 >> >> J400 100 >> >> >> On Fri, Jul 22, 2016 at 6:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 7/22/16 6:50 PM, Chang Woon Jang wrote: >>> >>> Dear Grimaces Users, >>>> >>>> I have the decomposition error. I have tried to reduce the number of >>>> cores >>>> but still have the same problem. In my conf.gro, the cell size is about >>>> 5.5x5.5x5.5 but I do not know what the minimum cell size of 1.875nm. >>>> >>>> Would you please give me some comments or relevant topics addressed? >>>> >>>> >>>> The .log file tells you how DD is being set up and what the the limiting >>> interactions are. Verify that your topology is sound from what the .log >>> tells you. >>> >>> ------------------------------------------------------- >>> >>>> >>>> Program gmx, VERSION 5.0.7-dev-20151003-1909f2f >>>> >>>> Source code file: >>>> >>>> /home1/02271/huddack/votca_install/src/gromacs/src/gromacs/mdlib/domdec.c, >>>> line: 6902 >>>> >>>> >>>> Also make sure your run isn't failing because of something due to hacked >>> code. Development versions generally shouldn't be used for >>> production-level >>> science. >>> >>> -Justin >>> >>> >>> Fatal error: >>>> >>>> There is no domain decomposition for 16 ranks that is compatible with >>>> the >>>> given box and a minimum cell size of 1.875 nm >>>> >>>> Change the number of ranks or mdrun option -rdd or -dds >>>> >>>> Look in the log file for details on the domain decomposition >>>> >>>> For more information and tips for troubleshooting, please check the >>>> GROMACS >>>> >>>> website at http://www.gromacs.org/Documentation/Errors >>>> >>>> ------------------------------------------------------- >>>> >>>> >>>> -- >>> ================================================== >>> >>> 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. >>> >>> > -- > ================================================== > > 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. > -- Best regards, Changwoon Jang, Postdoctoral Research Fellow Department of Chemical & Biological Engineering, Drexel University 3141 Chestnut Street, Philadelphia, PA 19104 Voice: (662) 617-2267 E-mail: cj...@drexel.edu -- 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.