[gmx-users] Error : There is no domain decomposition for 4 nodes that compatible with the given box

[Justin A. Lemkul]

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
> 

-- 
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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

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