<P> Hello, when I use the 2D periodic boundary for the pr run , it just ran several steps then exited, the log file has some error message like this :</P>
<P><EM>Program mdrun, VERSION 4.0.5<BR>Source code file: nsgrid.c, line: 357</EM></P>
<P><EM>Range checking error:<BR>Explanation: During neighborsearching, we assign each particle to a grid<BR>based on its coordinates. If your system contains collisions or parameter<BR>errors that give particles very high velocities you might end up with some<BR>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<BR>put these on a grid, so this is usually where we detect those errors.<BR>Make sure your system is properly energy-minimized and that the potential<BR>energy seems reasonable before trying again.</EM></P>
<P><EM>Variable ci has value -1. It should have been within [ 0 .. 432 ]</EM></P>
<P>If I use the 3D periodic boundary, it would be OK, but I have to use the 2D periodic boundary for my simulation, I don't know what is the reason. my pr.mdp file is below:</P>
<P><EM>title = 10tbppr<BR>cpp = /usr/bin/cpp <BR>define = -DPOSRES<BR>constraints = all-bonds<BR>integrator = md<BR>dt = 0.002 ; ps !<BR>nsteps = 30000 ; total 60.0 ps.<BR>nstcomm = 1<BR>nstxout = 100<BR>nstvout = 100<BR>nstfout = 0<BR>nstlog = 10<BR>nstenergy = 10<BR>nstlist = 5 <BR>ns_type = grid<BR>rlist = 1.0 <BR>; Eledtrostatics<BR>coulombtype = PME<BR>rcoulomb = 1.0 ;distance for the coulomb cut-off<BR>; VdW<BR>vdwtype = cut-off<BR>rvdw = 1.4 <BR>DispCorr = EnerPres<BR>;Ewald<BR>fourierspacing = 0.3<BR>fourier_nx = 0<BR>fourier_ny = 0<BR>fourier_nz = 0<BR>pme_order = 4<BR>ewald_rtol = 1e-5<BR>ewald_geometry = 3dc <BR>optimize_fft = yes<BR>;Pbc and walls<BR>pbc = xy ;ns_type must be grid<BR>nwall = 2<BR>wall_type = 10-4<BR>wall_atomtype = SI SI<BR>wall_density = 10 10<BR>wall_r_linpot = 0.5<BR>; Berendsen temperature coupling is on in three groups<BR>Tcoupl = v-rescale<BR>tau_t = 0.1 0.1 0.1<BR>tc_grps = SOL C12 TBP<BR>ref_t = 300 300 300<BR>; Pressure coupling is on<BR>Pcoupl = parrinello-rahman <BR>pcoupltype = semiisotropic<BR>tau_p = 0.5<BR>compressibility = 0 4.5e-5<BR>ref_p = 1.0 1.0<BR>; Generate velocites is on at 300 K.<BR>gen_vel = yes<BR>gen_temp = 300.0<BR>gen_seed = -1</EM></P>
<P><EM> </EM>could<EM> </EM>you help me analyze the reason? thank you very much !</P>