[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

Nilesh Dhumal ndhumal at andrew.cmu.edu
Mon Dec 7 00:28:21 CET 2009


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

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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