Dear gmx-users, I run MD for a protein molecule solvated with water molecules. Until now it works well, however strangely they started to crash, I don't know the reason. So, if anyone have similar problem please let me know the solution. It seems like that NPT system might cause some problems.
Also, when I continue MD further, it works. (Sometimes simulation crashes after 1 ns, but sometimes it crashes only after 100 ps.) Then, can I use those results for further studies? This is the mdp file: integrator = md nsteps = 1500000 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 310 310 pcoupl = Berendsen pcoupltype = isotropic tau-p = 1 ref-p = 1.0 compressibility = 4.5e-5 constraints = all-bonds constraint_algorithm = lincs nstxout = 1000 nstvout = 10000 nstxtcout = 100 nstenergy = 100 ; Generate velocity is on at 300 K gen_vel = yes gen_temp = 300.0 gen_seed = 173529 This is the error message: ------------------------------------------------------- Program mdrun_mpi_d, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 3185. It should have been within [ 0 .. 3072 ] Please report this to the mailing list ([email protected]) ------------------------------------------------------- "Interfacing Space and Beyond..." (P. J. Harvey) Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi_d on CPU 1 out of 16 gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey) [1] MPI Abort by user Aborting program ! [1] Aborting program! ------------------------------------------------------- -- -------------------------------------------------- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PROTECTED] [EMAIL PROTECTED]
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