[gmx-users] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.

[Lum Nforbi]

Hello all,

    After minimizing the energy of my system of 200 particle coordinates of
box dimension 3.5 nm to an acceptable value, I proceeded to doing mdrun but
got the error message:

"Source code file: nsgrid.c, line: 348. Fatal error: Number of grid cells is
zero. Probably the system and box collapsed."

I was wondering what could be the cause. Below are my energy minimization
parameter file, the results of the minimization and the mdrun parameter
file.

oxymin.mdp file

title                    = NPT simulation of a Lennard-Jones Fluid
cpp                      = /lib/cpp
include                  = -I../top
define                   =
constraints              = none
integrator               = steep
nsteps                   = 5000
emtol                    = 1000
emstep                   =
0.10
nstlist                  = 10
rlist                    = 0.9
ns_type                  = grid
coulombtype              = PME
rcoulomb                 = 0.9
vdwtype                  = cut-off
rvdw                     = 0.9
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 4
ewald_rtol               = 1e-05
optimize_fft             = yes

Step=  673, Dmax= 6.9e-03 nm, Epot=  6.11020e+05 Fmax= 7.64685e+03, atom= 19
Step=  675, Dmax= 4.1e-03 nm, Epot=  6.10956e+05 Fmax= 1.71624e+03, atom= 53
Step=  677, Dmax= 2.5e-03 nm, Epot=  6.10933e+05 Fmax= 3.60118e+03, atom= 30
Step=  678, Dmax= 3.0e-03 nm, Epot=  6.10927e+05 Fmax= 3.03499e+03, atom= 19
Step=  679, Dmax= 3.6e-03 nm, Epot=  6.10915e+05 Fmax= 4.80541e+03, atom= 30
Step=  680, Dmax= 4.3e-03 nm, Epot=  6.10913e+05 Fmax= 4.79865e+03, atom= 19
Step=  681, Dmax= 5.2e-03 nm, Epot=  6.10910e+05 Fmax= 6.50875e+03, atom= 30
Step=  683, Dmax= 3.1e-03 nm, Epot=  6.10857e+05 Fmax= 9.58182e+02, atom=
160

writing lowest energy coordinates.

Back Off! I just backed up oxymin.gro to ./#oxymin.gro.6#

Steepest Descents converged to Fmax < 1000 in 684 steps
Potential Energy  =  6.1085662e+05
Maximum force     =  9.5818250e+02 on atom 160
Norm of force     =  2.9207101e+02

oxymdrun.mdp file

title                    = NPT simulation of a LJ FLUID
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md         ; a leap-frog algorithm for
integrating Newton's equations of motion
dt                       = 0.002      ; time-step in ps
nsteps                   = 500000     ; total number of steps; total time (1
ns)

nstcomm                  = 1          ; frequency for com removal
nstxout                  = 1000       ; freq. x_out
nstvout                  = 1000       ; freq. v_out
nstfout                  = 0          ; freq. f_out
nstlog                   = 500        ; energies to log file
nstenergy                = 500        ; energies to energy file

nstlist                  = 10         ; frequency to update neighbour list
ns_type                  = grid       ; neighbour searching type
rlist                    = 0.9        ; cut-off distance for the short range
neighbour list

coulombtype              = PME        ; particle-mesh-ewald electrostatics
rcoulomb                 = 0.9        ; distance for the coulomb cut-off
vdw-type                 = Cut-off    ; van der Waals interactions
rvdw                     = 0.9        ; distance for the LJ or Buckingham
cut-off

fourierspacing           = 0.12       ; max. grid spacing for the FFT grid
for PME
fourier_nx               = 0          ; highest magnitude in reciprocal
space when using Ewald
fourier_ny               = 0          ; highest magnitude in reciprocal
space when using Ewald
fourier_nz               = 0          ; highest magnitude in reciprocal
space when using Ewald
pme_order                = 4          ; cubic interpolation order for PME
ewald_rtol               = 1e-5       ; relative strength of the
Ewald-shifted direct potential
optimize_fft             = yes        ; calculate optimal FFT plan for the
grid at start up.
DispCorr                 = no         ;

Tcoupl                   = nose-hoover; temp. coupling with vel. rescaling
with a stochastic term.
tau_t                    = 0.5        ; time constant for coupling
tc-grps                  = OXY        ; groups to couple separately to temp.
bath
ref_t                    = 80         ; ref. temp. for coupling

Pcoupl                   = parrinello-rahman  ; exponential relaxation
pressure coupling (box is scaled every timestep)
Pcoupltype               = isotropic  ; box expands or contracts evenly in
all directions (xyz) to maintain proper pressure
tau_p                    = 0.9        ; time constant for coupling (ps)
compressibility          = 4.5e-5     ; compressibility of solvent used in
simulation
ref_p                    = 1.0        ; ref. pressure for coupling (bar)

gen_vel                  = yes        ; generate velocities according to a
Maxwell distr. at gen_temp
gen_temp                 = 80         ; temperature for Maxwell distribution
gen_seed                 = 173529     ; used to initialize random generator
for random velocities

I appreciate your suggestions.

Lum
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