----- Original Message ----- From: ABEL Stephane 175950 <stephane.a...@cea.fr> Date: Thursday, September 30, 2010 21:21 Subject: [gmx-users] Error : There is no domain decomposition for To: gmx-users@gromacs.org
> Yeah Justin, I have already read the comments related to the > link before to post in the mailing list. But I don't know how to > correct this ? > > Increase/decrease the number of node or CPU ? No, you should address the underlying issue. You have a very long-range interaction. What is it, and why? > Initial maximum inter charge-group distances: > > two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107 > > multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106 > > Minimum cell size due to bonded interactions: 7.402 nm Mark > > Thank you again for your help > > Stephane > > ABEL Stephane 175950 wrote: > > Dear All, > > > > I am trying to do a MD of a system containing TIP3P water, a > peptide, some glycolipids molecule and ions in a cubic box. The > forcefield used is CHARMM and are taken from previous MD. The > bonded and nonbonded parameters was converted in GROMACS > manually because some parameters are not in present in current > GMX (v 4.5.1) distribution. > > > > I have minimized successfully the system. see below > > > > ---- em.mdp ------------------- > > > > title = bDM+KTM17 in water > > > > ; Preprocessor - specify a full path if necessary. > > > > cpp = cpp > > > > include = -I../top > > > > define = -DFLEXIBLE > > > > integrator = steep > > > > nstcgsteep = 5000 > > > > emstep = 0.01 > > > > emtol = 500.0 > > > > ;dt = 0.002 > > > > pbc = xyz > > > > nsteps = 5000 > > > > nstlist = 5 > > > > ns_type = grid > > > > rlist = 1.2 > > > > coulombtype = PME > > > > rcoulomb = 1.2 > > > > rvdw = 1.2 > > > > fourierspacing = 0.12 > > > > pme_order = 4 > > > > ewald_rtol = 1e-05 > > > > optimize_fft = yes > > > > ------------------- > > > > ---- Final results of energy minimization process > > > > Energies (kJ/mol) > > > > Bond Angle U-B Proper Dih. Improper Dih. > > > > 3.58212e+04 1.88051e+04 6.00353e+03 3.58404e+04 7.30187e+00 > > > > CMAP Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) > > > > -1.39601e+02 1.11718e+04 1.76772e+05 1.66576e+05 -1.30112e+06 > > > > Coul. recip. Potential Pressure (bar) > > > > -1.17090e+05 -9.67347e+05 0.00000e+00 > > > > Steepest Descents converged to Fmax < 500 in 107 steps > > > > Potential Energy = -9.67347283476003e+05 > > > > Maximum force = 4.75153618041724e+02 on atom 313 > > > > Norm of force = 9.37591893853129e+00 > > > > But when i try to equilibrate this system in NVT ensemble for > 100 ps with the md.mdp below > > > > ---- nvt.mdp ------------------- > > > > title = KTM17-bDM MD > > > > ;define = -DPOSRES ; position restrain the protein > > > > ; Run parameters > > > > integrator = md ; leap-frog integrator > > > > nsteps = 50000 ; 2 * 50000 = 100 ps > > > > dt = 0.002 ; 2 fs > > > > ; Output control > > > > nstxout = 100 ; save coordinates every 0.2 ps > > > > nstvout = 100 ; save velocities every 0.2 ps > > > > nstenergy = 100 ; save energies every 0.2 ps > > > > nstlog = 100 ; update log file every 0.2 ps > > > > ; Bond parameters > > > > continuation = no ; first dynamics run > > > > constraint_algorithm = lincs ; holonomic constraints > > > > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained> > > lincs_iter = 1 ; accuracy of LINCS > > > > lincs_order = 4 ; also related to accuracy > > > > ; Neighborsearching > > > > vdw-type = cut-off > > > > ns_type = grid ; search neighboring grid cels > > > > nstlist = 5 ; 10 fs > > > > rlist = 1.2 ; short-range neighborlist cutoff (in nm) > > > > rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) > > > > rvdw = 1.2 ; short-range van der Waals cutoff (in nm) > > > > ; Electrostatics > > > > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics> > > pme_order = 4 ; cubic interpolation > > > > fourierspacing = 0.12 ; grid spacing for FFT > > > > ; Temperature coupling is on > > > > tcoupl = V-rescale ; modified Berendsen thermostat > > > > tc-grps = System ; one coupling groups - more accurate > > > > tau_t = 0.1 ; time constant, in ps > > > > ref_t = 300 ; reference temperature, one for each group, in K > > > > ; Pressure coupling is off > > > > pcoupl = no ; no pressure coupling in NVT > > > > ; Periodic boundary conditions > > > > pbc = xyz ; 3-D PBC > > > > ; Dispersion correction > > > > DispCorr = EnerPres ; account for cut-off vdW scheme > > > > ; Velocity generation > > > > gen_vel = yes ; assign velocities from Maxwell distribution > > > > gen_temp = 300 ; temperature for Maxwell distribution > > > > gen_seed = -1 ; generate a random seed > > > > ------------- > > > > I obtain the following error with mdrun_mpi command > > > > /usr/pbs/bin/mpiexec mdrun_mpi -s hMRP1_K-TM17_md.tpr -o > hMRP1_K-TM17_md.trr -c hMRP1_K-TM17_md.gro -e hMRP1_K- > TM17_bDM_h2o_Cl_md.edr -g hMRP1_K-TM17_bDM_h2o_Cl_md.log > > > > ------ error > > > > Initializing Domain Decomposition on 4 nodes > > > > Dynamic load balancing: auto > > > > Will sort the charge groups at every domain (re)decomposition > > > > Initial maximum inter charge-group distances: > > > > two-body bonded interactions: 6.729 nm, LJ-14, atoms 11100 11107 > > > > multi-body bonded interactions: 6.729 nm, U-B, atoms 11100 11106 > > > > Minimum cell size due to bonded interactions: 7.402 nm > > > > Maximum distance for 5 constraints, at 120 deg. angles, all- > trans: 0.819 nm > > > > Estimated maximum distance required for P-LINCS: 0.819 nm > > > > Using 0 separate PME nodes > > > > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > > > > Optimizing the DD grid for 4 cells with a minimum initial size > of 9.252 nm > > > > The maximum allowed number of cells is: X 0 Y 0 Z 0 > > > > ------------------------------------------------------- > > > > Program mdrun_mpi, VERSION 4.5.1 > > > > Source code file: domdec.c, line: 6428 > > > > Fatal error: > > > > There is no domain decomposition for 4 nodes that is > compatible with the given box and a minimum cell size of 9.25216 nm > > > > Change the number of nodes 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 > > > > ------------------------------------------------------- > > > > "Player Sleeps With the Fishes" (Ein Bekanntes Spiel Von ID > Software)> > > I have also checked the mimized structure at different > minimization step, and I saw no problems. > > > > I don't know what is problem here. Could you help me ? > > > > http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm > > -Justin > > > Thank you in advance for your advices and comments. > > > > Stephane > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? 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