[gmx-users] mdrun Fatal error: Domain decomposition does not support simple neighbor searching

[shivangi nangia]

Dear gmx-users,

I have a cube (8 nm)  of the system containing 1:1 :: water: methanol, a
polypeptide, Li ions and 2,5-dihydroxybenzoic acid anions.
I am heating this system with no PBC ( evaporation).

The md.mdp file is:

; Run parameters
integrator  = md     ; leap-frog integrator
nsteps      = 250000 ; 2 * 250000 = 500 ps, 0.5 ns
dt    = 0.002     ; 2 fs
; Output control
nstxout     = 1000      ; save coordinates every 2 ps
nstvout     = 1000      ; save velocities every 2 ps
nstxtcout   = 1000      ; xtc compressed trajectory output every 2 ps
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
; Bond parameters
continuation   = yes    ; Restarting after NVT
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     = simple *
nstlist     = 5      ; 10 fs
rlist    = 1.0    ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0    ; short-range electrostatic cutoff (in nm)
rvdw     = 1.0    ; short-range van der Waals cutoff (in nm)
; Electrostatics
;coulombtype = PME    ; Particle Mesh Ewald for long-range electrostatics
;pme_order   = 4      ; cubic interpolation
;fourierspacing = 0.16      ; grid spacing for FFT
; Temperature coupling is on
tcoupl      = V-rescale ; modified Berendsen thermostat
tc-grps     = Protein Non-Protein   ; two coupling groups - more accurate
tau_t    = 0.1 0.1   ; time constant, in ps
ref_t    = 500    500   ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl      = no
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      = no  *  ; 3-D PBC
; Dispersion correction
DispCorr = no  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no     ; Velocity generation is off
;comm_mode
comm_mode = ANGULAR


I have run this system in past without any errors, suddenly I am constantly
running into the following error if I submit my job on a cluster in que *(
interactive runs fine)*


Fatal error:
Domain decomposition does not support simple neighbor searching, use grid
searching or use particle decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


With pbc = no the only grid type an be used is simple.
I tried changing the size of the cube but I still face the same problem.

I am unable to understand what could be going wrong suddenly.

Please guide

Thanks in advance,
SN
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