Yes sir, even though its not working
On Sun, Apr 17, 2016 at 9:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/17/16 11:35 AM, REMYA R wrote: > >> Dear sir, >> >> I am getting error while running simulation of Protein-Ligand complex , >> usong GROMOS force field, spc water model at the equilibration phase of >> bevan lab tutorial for protein-ligand simulation, version 4.6.1 ( >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/06_equil.html >> ) >> >> Here below I am pasting some information from em.log >> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S >> >> av. #atoms communicated per step for force: 2 x 48020.5 >> >> >> R E A L C Y C L E A N D T I M E A C C O U N T I N G >> >> Computing: Nodes Number G-Cycles Seconds % >> ----------------------------------------------------------------------- >> Domain decomp. 15 152 11.010 2.4 4.9 >> DD comm. load 15 1 0.004 0.0 0.0 >> Send X to PME 15 125 0.069 0.0 0.0 >> Comm. coord. 15 125 5.553 1.2 2.5 >> Neighbor search 15 125 21.088 4.6 9.4 >> Force 15 125 21.412 4.6 9.6 >> Wait + Comm. F 15 125 20.474 4.4 9.2 >> PME mesh 9 125 19.929 4.3 8.9 >> Wait + Comm. X/F 9 31.486 6.8 14.1 >> Wait + Recv. PME F 15 125 1.507 0.3 0.7 >> Constraints 15 249 1.062 0.2 0.5 >> Comm. energies 15 125 2.644 0.6 1.2 >> Rest 15 87.106 18.9 39.0 >> ----------------------------------------------------------------------- >> Total 24 223.343 48.4 100.0 >> ----------------------------------------------------------------------- >> ----------------------------------------------------------------------- >> PME redist. X/F 9 250 4.982 1.1 2.2 >> PME spread/gather 9 250 6.790 1.5 3.0 >> PME 3D-FFT 9 250 5.999 1.3 2.7 >> PME solve 9 125 2.152 0.5 1.0 >> ----------------------------------------------------------------------- >> >> Parallel run - timing based on wallclock. >> >> NODE (s) Real (s) (%) >> Time: 2.016 2.016 100.0 >> (Mnbf/s) (GFlops) (steps/hour) >> Performance: 337.723 47.730 223242.7 >> Finished mdrun on node 0 Thu Apr 14 19:38:14 2016 >> >> I am new user for this simulation, could you please help me to rectify >> this >> error.Below I am pasting the error message that I got, >> *Fatal error:* >> A charge group moved too far between two domain decomposition steps >> This usually means that your system is not well equilibrated >> >> > Have you tried Google? This error comes up almost daily on this list... > > -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? 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.