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 Thank you in advance -- 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.