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

[ABEL Stephane 175950]

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 ?

Thank you in advance for your advices and comments.

Stephane