Hello all,<br><br> 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:<br><br>"Source code file: nsgrid.c, line: 348. Fatal error: Number of grid cells is zero. Probably the system and box collapsed." <br>
<br>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.<br><br>oxymin.mdp file<br><br>title = NPT simulation of a Lennard-Jones Fluid<br>
cpp = /lib/cpp<br>include = -I../top<br>define = <br>constraints = none<br>integrator = steep<br>nsteps = 5000<br>emtol = 1000<br>
emstep = 0.10 <br>nstlist = 10<br>rlist = 0.9<br>ns_type = grid<br>coulombtype = PME<br>
rcoulomb = 0.9<br>vdwtype = cut-off<br>rvdw = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>
pme_order = 4<br>ewald_rtol = 1e-05<br>optimize_fft = yes<br><br>Step= 673, Dmax= 6.9e-03 nm, Epot= 6.11020e+05 Fmax= 7.64685e+03, atom= 19<br>Step= 675, Dmax= 4.1e-03 nm, Epot= 6.10956e+05 Fmax= 1.71624e+03, atom= 53<br>
Step= 677, Dmax= 2.5e-03 nm, Epot= 6.10933e+05 Fmax= 3.60118e+03, atom= 30<br>Step= 678, Dmax= 3.0e-03 nm, Epot= 6.10927e+05 Fmax= 3.03499e+03, atom= 19<br>Step= 679, Dmax= 3.6e-03 nm, Epot= 6.10915e+05 Fmax= 4.80541e+03, atom= 30<br>
Step= 680, Dmax= 4.3e-03 nm, Epot= 6.10913e+05 Fmax= 4.79865e+03, atom= 19<br>Step= 681, Dmax= 5.2e-03 nm, Epot= 6.10910e+05 Fmax= 6.50875e+03, atom= 30<br>Step= 683, Dmax= 3.1e-03 nm, Epot= 6.10857e+05 Fmax= 9.58182e+02, atom= 160<br>
<br>writing lowest energy coordinates.<br><br>Back Off! I just backed up oxymin.gro to ./#oxymin.gro.6#<br><br>Steepest Descents converged to Fmax < 1000 in 684 steps<br>Potential Energy = 6.1085662e+05<br>Maximum force = 9.5818250e+02 on atom 160<br>
Norm of force = 2.9207101e+02<br><br>oxymdrun.mdp file<br><br>title = NPT simulation of a LJ FLUID<br>cpp = /lib/cpp<br>include = -I../top<br>define = <br>
integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion<br>dt = 0.002 ; time-step in ps<br>nsteps = 500000 ; total number of steps; total time (1 ns)<br>
<br>nstcomm = 1 ; frequency for com removal<br>nstxout = 1000 ; freq. x_out<br>nstvout = 1000 ; freq. v_out<br>nstfout = 0 ; freq. f_out<br>
nstlog = 500 ; energies to log file<br>nstenergy = 500 ; energies to energy file<br> <br>nstlist = 10 ; frequency to update neighbour list<br>
ns_type = grid ; neighbour searching type<br>rlist = 0.9 ; cut-off distance for the short range neighbour list<br><br>coulombtype = PME ; particle-mesh-ewald electrostatics<br>
rcoulomb = 0.9 ; distance for the coulomb cut-off<br>vdw-type = Cut-off ; van der Waals interactions<br>rvdw = 0.9 ; distance for the LJ or Buckingham cut-off<br>
<br>fourierspacing = 0.12 ; max. grid spacing for the FFT grid for PME<br>fourier_nx = 0 ; highest magnitude in reciprocal space when using Ewald<br>fourier_ny = 0 ; highest magnitude in reciprocal space when using Ewald<br>
fourier_nz = 0 ; highest magnitude in reciprocal space when using Ewald<br>pme_order = 4 ; cubic interpolation order for PME<br>ewald_rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential<br>
optimize_fft = yes ; calculate optimal FFT plan for the grid at start up.<br>DispCorr = no ; <br><br>Tcoupl = nose-hoover; temp. coupling with vel. rescaling with a stochastic term.<br>
tau_t = 0.5 ; time constant for coupling<br>tc-grps = OXY ; groups to couple separately to temp. bath<br>ref_t = 80 ; ref. temp. for coupling<br>
<br>Pcoupl = parrinello-rahman ; exponential relaxation pressure coupling (box is scaled every timestep)<br>Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure<br>
tau_p = 0.9 ; time constant for coupling (ps)<br>compressibility = 4.5e-5 ; compressibility of solvent used in simulation<br>ref_p = 1.0 ; ref. pressure for coupling (bar)<br>
<br>gen_vel = yes ; generate velocities according to a Maxwell distr. at gen_temp<br>gen_temp = 80 ; temperature for Maxwell distribution<br>gen_seed = 173529 ; used to initialize random generator for random velocities<br>
<br>I appreciate your suggestions.<br><br>Lum<br>