[gmx-users] Software inconsistency error: One or more interactions were multiple assigned in the domain decomposition

[Olivia Waring]

Hi Gromacs users,

My invocation of mdrun, using 8 processors and the following mdp file:


title           = Alkanethiol SAM MD
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 500000        ; 25 * 40 = 1000 ps, 1 ns (actually .2ns
now)
dt              = 0.001         ; .5 fs (changed from 2.5)
; Output control
nstxout         = 1             ; save coordinates every 2 ps
nstvout         = 100           ; save velocities every 2 ps
nstxtcout       = 100           ; xtc compressed trajectory output every 2
ps
nstenergy       = 100           ; save energies every 2 ps
nstlog          = 100           ; update log file every 2 ps
nstfout         = 100           ; save forces every .1 ps
; Bond parameters
continuation    = yes           ; Restarting after NPT
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
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.4           ; short-range neighborlist cutoff (in nm)
coulombtype     = Cut-off
rcoulomb        = 1.4           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.4           ; short-range van der Waals cutoff (in nm)
; Electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; ewald summation
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = System        ; two 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 on
;pcoupl         = Parrinello-Rahman     ; Pressure coupling on in NPT
;pcoupltype     = isotropic     ; uniform scaling of box vectors
;tau_p          = 2.0           ; time constant, in ps
;ref_p          = 1.0           ; reference pressure, in bar
;compressibility = 4.5e-5       ; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off
; Non-equilibrium MD
freezegrps      = S DIO
freezedim       = Y Y Y N N Y           ; frozen in all three dimensions



generated the following error message:



There are: 1184 Atoms
Charge group distribution at step 0: 30 36 45 54 180 211 216 252 30 34 45 51
Grid: 3 x 4 x 4 cells
Initial temperature: 0 K

Started mdrun on node 0 Fri Apr 20 08:41:31 2012

           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    3.19470e+03    8.21460e+00    8.87579e+01    0.00000e+00   -5.95420e+03
  Disper. corr.   Coulomb (SR)      Potential    Kinetic En.   Total Energy
   -1.10584e+01    0.00000e+00   -2.67358e+03    1.60252e+03   -1.07106e+03
  Conserved En.    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -1.07106e+03    1.76581e+02   -5.03783e-01   -3.74984e+04    2.18772e-06

DD  step 4 load imb.: force 181.0%

Not all bonded interactions have been properly assigned to the domain
decomposition cells

A list of missing interactions:
               Angle of   1001 missing   -158
      Ryckaert-Bell. of    910 missing   -211
               LJ-14 of    910 missing   -270

Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
      Ryckaert-Bell. atoms  279  280  281  282 global   279   280   281
282
      Ryckaert-Bell. atoms  303  304  305  306 global   303   304   305
306
               Angle atoms  304  305  306      global   304   305   306
      Ryckaert-Bell. atoms  304  305  306  307 global   304   305   306
307
      Ryckaert-Bell. atoms  316  317  318  319 global   316   317   318
319
               Angle atoms  317  318  319      global   317   318   319
      Ryckaert-Bell. atoms  317  318  319  320 global   317   318   319
320
      Ryckaert-Bell. atoms  344  345  346  347 global   344   345   346
347
      Ryckaert-Bell. atoms  485  486  487  488 global   485   486   487
488
               Angle atoms  486  487  488      global   486   487   488

-------------------------------------------------------
Program mdrun, VERSION 4.5.4
Source code file: domdec_top.c, line: 352

Software inconsistency error:
One or more interactions were multiple assigned in the domain decompostion
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------



I am having trouble tracking down the source of the error - the
documentation on this sort of thing is sparse.

Thanks so much in advance,



-- 
Olivia Waring
Princeton University '12
AB Chemistry
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