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

[Mark Abraham]

On 1/08/2012 1:06 PM, leila karami wrote:
> 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)?

Standard advice is here 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

You should pay particular attention to what it says about the use of 
pressure coupling.

Mark

>
> 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.