Dear Justin, Search engine give a clue about using -nt options. However, how to choose the proper number for -nt option from the error message?
Thank you. Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 12:02 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/30/16 11:52 AM, Chang Woon Jang wrote: > >> Dear Justin Lemkul, >> >> Thank you for your answers. The following is the error message after I >> run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd >> 2.5". >> >> >> Initializing Domain Decomposition on 8 ranks >> Dynamic load balancing: auto >> Will sort the charge groups at every domain (re)decomposition >> Minimum cell size due to bonded interactions: 2.500 nm >> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 >> Optimizing the DD grid for 8 cells with a minimum initial size of 3.125 nm >> The maximum allowed number of cells is: X 1 Y 1 Z 1 >> >> ------------------------------------------------------- >> Program gmx, VERSION 5.0.8-dev-20151014-1f04b58 >> Source code file: >> /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec.c, line: >> 6902 >> >> Fatal error: >> There is no domain decomposition for 8 ranks that is compatible with the >> given box and a minimum cell size of 3.125 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 >> ------------------------------------------------------- >> >> > And what does Google tell you about this particular case? Hint: the same > error gets posted to this list pretty much weekly, if not more often. It's > been rationalized and solved time and time again. > > -Justin > > > >> Best regards, >> Changwoon Jang >> >> >> On Tue, Aug 30, 2016 at 11:30 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 8/30/16 10:41 AM, Chang Woon Jang wrote: >>> >>> Dear Justin Lemkul, >>>> Thank you for your response. Yes, I use coarse-grained system >>>> (thermosetting polymer). I prepared the system from the equilibrated >>>> atomistic system. The atomistic system was equilibrated using OPLS-AA >>>> force >>>> filed under NPT and NVT for almost 40 ns. The initial atomistic system >>>> contained 13854 atoms. The equilibrated atomistic system was >>>> coarese-grained (mapped) with certain criteria. Now, I am trying to get >>>> CG >>>> potentials using iterative Boltzmann Inversion, but this error keeps me >>>> dizzy. >>>> >>>> Whenever I use -rdd options, it gives another error like domain >>>> decomposition error with other options recommended. Whenever I use -nt >>>> >>>> >>> Please always post exact error messages, copied and pasted directly from >>> the terminal or .log file. We can't guess at what you're reading. >>> >>> options, the simulation goes well but the simulation trajectory seem >>> weird >>> >>>> that some molecules are going out the simulation box >>>> >>>> >>>> This is just PBC. There is no "outside" of a box. If you've got >>> polymers, they will elongate and contract depending on their physical >>> behavior. There's nothing wrong with that. >>> >>> -Justin >>> >>> >>> It seems tricky to find what is the problem. >>> >>>> >>>> Thank you. >>>> >>>> Best regards, >>>> Changwoon Jang >>>> >>>> On Tue, Aug 30, 2016 at 8:37 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> >>>>> On 8/29/16 6:02 PM, Chang Woon Jang wrote: >>>>> >>>>> Dear Gromacs Users, >>>>> >>>>>> >>>>>> >>>>>> I have a Fatal error as follow. The error says -rdd option or >>>>>> -ddcheck. >>>>>> How >>>>>> can I properly use these options? Is the following command the proper >>>>>> use >>>>>> of these options? >>>>>> >>>>>> gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5 >>>>>> >>>>>> >>>>>>> -ddcheck >>>>>>> >>>>>> >>>>>> >>>>>> Yes, but note that -ddcheck is on by default anyway, and you should >>>>>> look >>>>>> >>>>> into why this might be happening. You can get around this error, but >>>>> it >>>>> often indicates instability. Without a complete description of what >>>>> your >>>>> system is, what you've previously done to prepare, minimize, >>>>> equilibrate, >>>>> etc. we're sort of just guessing here. If the system is coarse grain, >>>>> then >>>>> use of a large -rdd is typical (as you will see from many threads in >>>>> the >>>>> archive that address this case specifically). >>>>> >>>>> -Justin >>>>> >>>>> Thank you. >>>>> >>>>> >>>>>> >>>>>> 1 of the 1612 bonded interactions could not be calculated because some >>>>>> atoms involved moved further apart than the multi-body cut-off >>>>>> distance >>>>>> (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, >>>>>> for >>>>>> pairs and tabulated bonds also see option -ddcheck >>>>>> For more information and tips for troubleshooting, please check the >>>>>> GROMACS >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Best regards, >>>>>> Changwoon Jang, >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>> ================================================== >>>>> >>>>> 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. >>> >>> > -- > ================================================== > > 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? 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.