[gmx-users] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 10 19:54:55 CET 2010
Lum Nforbi wrote:
> 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."
>
Your system is blowing up:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
See additional comments below.
> 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
>
You have a reasonable Fmax, but the extremely high potential energy indicates
strong repulsive interactions within your system.
> 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)
>
Your coupling time is somewhat stringent (0.9 ps) - how did you choose this
value? tau_p might be more appropriately set somewhere between 2 and 10 ps for
Parrinello-Rahman.
The other option is that your underlying model for the system is faulty.
Consider the parameters you're applying to the particles.
-Justin
> 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
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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