[gmx-users] Error : There is no domain decomposition for

Thu Sep 30 13:27:11 CEST 2010

----- Original Message -----
From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
Date: Thursday, September 30, 2010 21:21
Subject: [gmx-users] Error : There is no domain decomposition for
To: gmx-users at 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
> 
> ========================================
> 
> > -- 
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