[gmx-users] Fatal error: 1 particles communicated to PME node 1 are more than a cell length out of the do main decomposition cell of their charge group

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> 
>  I am trying to a run a simulation for dioxin and ionic liquid system
> (BMI-DCN) in Gromacs 4.0.5 version.  The  minimization and equilibration
> (I heat the system at 700, 600, 500 (200 ps, NVT).  I run 1 ns for NVT
> and 4 ns for NPT) went OK. I am trying to run dynamics for 20 ns but
> after 3.5 ns I am getting following error.
> Fatal error: 1 particles communicated to PME node 1 are more than a cell
> length out of the do main decomposition cell of their charge group
> 

Please see here:

http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group

The standard advice for blowing up applies.  Potentially at fault: lousy 
parameters, insufficient minimization, and the fact that pressure coupling 
algorithms do not always deal well with high temperature (potentially very 
relevant for your setup).

-Justin

> Here I have pasted my md.mdp file
> 
> Nilesh
> 
> title               =  cpeptide MD
> cpp                 =  /usr/bin/cpp
> constraints         =  none
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  20000000     ; total 5 ps.
> nstcomm             =  1
> nstxout             =  50
> nstvout             =  0
> nstfout             =  0
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.4
> coulombtype         = PME
> vdwtype             = cut-off
> pbc                 = xyz
> fourierspacing      = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order           = 4
> optimize_fft        = yes
> ; Berendsen temperature coupling is on
> Tcoupl = v-rescale
> tau_t = 0.1
> tc-grps  =system
> ref_t =   400
> ; Pressure coupling is  on
> Pcoupl              = parrinello-rahman
> pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  400.0
> gen_seed            =  173529
> 
> 
> 

-- 
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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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