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

[leila karami]

Dear gromacs user

I did simulation of carbon nanotube (one in center and 6 in the
vicinity of that)|:

every CNT have 120 atoms.

1) energy minimization
2) equilibration in NVT ensemble

when I did equilibration in NPT ensemble, I encountered Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

How to solve this problem (with which parameter in the mdp file I can
solve this problem)?

Is there problem in the force field parameters?

If this problem resolves, can I do simulation under these conditions
but in the high pressure
or tempreture (800 bar or 1800 K)?

mdp file for equilibration in NPT ensemble is as follows:

title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.001; ps !
nsteps              =  50000    ; total (2 ns).
nstcomm             =  1
nstxout             =  100
nstxtcout           =  100
nstvout             =  100
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  0.8
rcoulomb            =  0.8
rvdw                =  0.8
; Electrostatics
coulombtype         =  Cut-off
; vdw
vdwtype             =  Cut-off
; Berendsen temperature coupling is on in two groups
Tcoupl              =  Nose-Hoover
tc-grps                = (NU    center
tau_t               =  0.10  0.10
ref_t               =  1300  1300
; Energy monitoring
energygrps          =  (NU     center
; Isotropic pressure coupling is now on
Pcoupl              =  Parrinello-Rahman
Pcoupltype          =  isotropic
tau_p               =  1
compressibility     =  4.5e-5
ref_p               =  1
; Generate velocites is off at 1300 K
gen_vel             =  no
; Periodic boundary conditions
pbc                    = xyz
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle          = 90
; Non-equilibrium MD
freezegrps           = (NU     center
freezedim            = N N N    Y Y Y


Any help will highly appreciated.