[gmx-users] no domain decomposition error while simulating membrane protein

[Kutzner, Carsten]

Dear Shabana,

which version of GROMACS are you using?

Carsten


> On 06 Aug 2015, at 11:24, shabana yasmeen <shabana.yasmeen90 at gmail.com> wrote:
> 
> Dear users!
> 
> I am working on membrane protein simulation  but at volume coupling I get
> error of no main decomposition.. I tried alot but it ended with same error
> every time. Hardware of computer is 16 core..
> here is nvt.mdp file
> 
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.0002    ;
> ; 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
> energygrps  = Protein Non-Protein
> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = H-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     = 10         ; 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  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> 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       = 300   300                     ; reference temperature,
> one for each group, in K
> ; Pressure coupling
> 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
> 
> 
> 
> 
> 
> Regards
> Shabana Yasmeen
> -- 
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