All, I'm trying to run a tabulated soft core potential with the form V = A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential after this.
I've chosen the parameters of this equation to be the same for all atoms in my system (a polymer containing carbon, nitrogen and hydrogen). I've not assigned any charges to the system. Running on Gromacs version 4.5.4 single precision on a high perfomance computing cluster the first 50 or so steps run fine, energies seem reasonable but then the simulation crashes with a segmentation fault. I submitted the job using the comand mdrun -table table.xvg -v -nt $NSLOTS -pd The job seems to run ok on my own desktop PC although I've not tried running it for more than a few minutes to check that it would indeed run. If anyone can tell me why this won't run on the computing cluster I'd appreciate it. the first few lines of my table file look like this: 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1500000E+05 0.0000000E+00 0.2000000E-02 0.0000000E+00 0.0000000E+00 0.3045913E-01 -0.4568869E+02 0.1499547E+05 0.4525801E+04 0.4000000E-02 0.0000000E+00 0.0000000E+00 0.2436730E+00 -0.1827548E+03 0.1498190E+05 0.9051602E+04 0.6000000E-02 0.0000000E+00 0.0000000E+00 0.8223965E+00 -0.4111982E+03 0.1495927E+05 0.1357740E+05 0.8000000E-02 0.0000000E+00 0.0000000E+00 0.1949384E+01 -0.7310191E+03 0.1492759E+05 0.1810320E+05 0.1000000E-01 0.0000000E+00 0.0000000E+00 0.3807391E+01 -0.1142217E+04 0.1488685E+05 0.2262901E+05 0.1200000E-01 0.0000000E+00 0.0000000E+00 0.6579172E+01 -0.1644793E+04 0.1483707E+05 0.2715481E+05 0.1400000E-01 0.0000000E+00 0.0000000E+00 0.1044748E+02 -0.2238746E+04 0.1477824E+05 0.3168061E+05 0.1600000E-01 0.0000000E+00 0.0000000E+00 0.1559507E+02 -0.2924076E+04 0.1471035E+05 0.3620641E+05 0.1800000E-01 0.0000000E+00 0.0000000E+00 0.2220471E+02 -0.3700784E+04 0.1463341E+05 0.4073221E+05 0.2000000E-01 0.0000000E+00 0.0000000E+00 0.3045913E+02 -0.4568869E+04 0.1454742E+05 0.4525801E+05 0.2200000E-01 0.0000000E+00 0.0000000E+00 0.4054110E+02 -0.5528332E+04 0.1445238E+05 0.4978381E+05 This is my mdp file (note that I turned dispersion correction off to see if this was the problem but it would seem that it is not): ; VARIOUS PREPROCESSING OPTIONS title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ;md for simulation, steep for Emin ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps =100000; 1000000 ;for simulation ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 100 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 50 nstenergy = 50 ; Output frequency and precision for xtc file nstxtcout = 50 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = user rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = user ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ;EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 2.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = no ;berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 ; OPTIONS FOR BONDS ;constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl =
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