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

[Justin A. Lemkul]

shivangi nangia wrote:
> 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)*
> 

Are the Gromacs versions the same?

> 
> 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.
> 

The issue is not related to system size.

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

The error is pretty clear.  With simple searching, you have to run either in 
serial or using particle decomposition (mdrun -pd).  As to why your input used 
to work and now suddenly doesn't, consult your system administrator.  No one 
here can likely answer this.  Sounds like someone's been playing with the 
system-wide Gromacs installation such that you're not using the same version you 
used to be, although I can't recall if/when DD ever supporting using simple 
neighbor searching.

-Justin

> Please guide
> 
> Thanks in advance,
> SN
> 
> 
> 

-- 
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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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