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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