[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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