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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