2008/8/5 Justin A. Lemkul <[EMAIL PROTECTED]> > > > Alexandr Malafeev wrote: > >> Hi Gromacs Users, >> >> In my simulation I have use very complicated potential, I obtained this >> potential from Boltzman Inversion of rdf, but when I trying run simulation I >> get error >> >> 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. >> >> Can you help me? >> > > There are two potential sources of error here. Either there is something > wrong with the potential function you're using (i.e., a typo or > miscalculation) or you have a physically unrealistic system. Did you do > energy minimization, and did it converge to an appropriate potential energy, > as the mdrun output says? > > Without knowing more about your system or the run parameters, it is > difficult to give more details. > > -Justin > > >> Thanks in advance. >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Yes I done energy minimization, and mdrun output here: Steepest Descents converged to machine precision in 17 steps, but did not reach the requested Fmax < 10. Potential Energy = -1.6686725e+06 Maximum force = 2.4212272e+07 on atom 5 Norm of force = 3.4130568e+07 other files from my system here too. It is chain cosist 5 coarse-grained units, in initial conformation there are two parallel chains on distance nm. ==============ffgmx.itp======================== [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 [ atomtypes ] B 337.000 0.000 A 4.275 2.14 [ bondtypes ] ; i j func b0 kb B B 1 1.3 1105.7 ; gaussian [ angletypes ] B B B 1 170.7 33.4 [ dihedraltypes ] B B B B 1 164.9 0.87 1 [ nonbond_params ] ;i j C6 C12 B B 1 4.275 2.14 [ pairtypes ] ;i j C6 C12 B B 1 4.275 2.14 =====================table.xvg=============================== 0 0.0 0.0 5.31525e-317 0.0 0.0 0.0 0.0505051 0.0 0.0 2.72297e 0.0 0.0 0.0 0.10101 0.0 0.0 6.64787e 0.0 0.0 0.0 0.151515 0.0 0.0 5.12363e 0.0 0.0 0.0 0.20202 0.0 0.0 1.6228e 0.0 0.0 0.0 0.252525 0.0 0.0 1.11475e 0.0 0.0 0.0 0.30303 0.0 0.0 1.24898e 0.0 0.0 0.0 0.353535 0.0 0.0 195960 0.0 0.0 0.0 0.40404 0.0 0.0 39279.7 0.0 0.0 0.0 0.454545 0.0 0.0 9471.18 0.0 0.0 0.0 0.505051 0.0 0.0 2632.59 0.0 0.0 0.0 0.555556 0.0 0.0 816.605 0.0 0.0 0.0 0.606061 0.0 0.0 275.131 0.0 0.0 0.0 0.656566 0.0 0.0 98.1504 0.0 0.0 0.0 0.707071 0.0 0.0 36.0257 0.0 0.0 0.0 0.757576 0.0 0.0 13.0521 0.0 0.0 0.0 0.808081 0.0 0.0 4.28676 0.0 0.0 0.0 0.858586 0.0 0.0 0.929196 0.0 0.0 0.0 0.909091 0.0 0.0 -0.30352 0.0 0.0 0.0 0.959596 0.0 0.0 -0.690878 0.0 0.0 0.0 1.0101 0.0 0.0 -0.747432 0.0 0.0 0.0 1.06061 0.0 0.0 -0.683641 0.0 0.0 0.0 1.11111 0.0 0.0 -0.585339 0.0 0.0 0.0 1.16162 0.0 0.0 -0.486288 0.0 0.0 0.0 1.21212 0.0 0.0 -0.398389 0.0 0.0 0.0 1.26263 0.0 0.0 -0.324521 0.0 0.0 0.0 1.31313 0.0 0.0 -0.264044 0.0 0.0 0.0 1.36364 0.0 0.0 -0.21515 0.0 0.0 0.0 1.41414 0.0 0.0 -0.175831 0.0 0.0 0.0 1.46465 0.0 0.0 -0.144252 0.0 0.0 0.0 1.51515 0.0 0.0 -0.118857 0.0 0.0 0.0 1.56566 0.0 0.0 -0.0983815 0.0 0.0 0.0 1.61616 0.0 0.0 -0.0818131 0.0 0.0 0.0 1.66667 0.0 0.0 -0.0683514 0.0 0.0 0.0 1.71717 0.0 0.0 -0.0573661 0.0 0.0 0.0 1.76768 0.0 0.0 -0.0483612 0.0 0.0 0.0 1.81818 0.0 0.0 -0.0409463 0.0 0.0 0.0 1.86869 0.0 0.0 -0.0348131 0.0 0.0 0.0 1.91919 0.0 0.0 -0.0297176 0.0 0.0 0.0 1.9697 0.0 0.0 -0.025466 0.0 0.0 0.0 2.0202 0.0 0.0 -0.0219036 0.0 0.0 0.0 2.07071 0.0 0.0 -0.0189067 0.0 0.0 0.0 2.12121 0.0 0.0 -0.0163756 0.0 0.0 0.0 2.17172 0.0 0.0 -0.0142297 0.0 0.0 0.0 2.22222 0.0 0.0 -0.0124039 0.0 0.0 0.0 2.27273 0.0 0.0 -0.010845 0.0 0.0 0.0 2.32323 0.0 0.0 -0.00950938 0.0 0.0 0.0 2.37374 0.0 0.0 -0.00836141 0.0 0.0 0.0 2.42424 0.0 0.0 -0.00737164 0.0 0.0 0.0 2.47475 0.0 0.0 -0.00651568 0.0 0.0 0.0 2.52525 0.0 0.0 -0.0057733 0.0 0.0 0.0 2.57576 0.0 0.0 -0.00512764 0.0 0.0 0.0 2.62626 0.0 0.0 -0.00456457 0.0 0.0 0.0 2.67677 0.0 0.0 -0.00407227 0.0 0.0 0.0 2.72727 0.0 0.0 -0.00364076 0.0 0.0 0.0 2.77778 0.0 0.0 -0.00326162 0.0 0.0 0.0 2.82828 0.0 0.0 -0.00292772 0.0 0.0 0.0 2.87879 0.0 0.0 -0.002633 0.0 0.0 0.0 2.92929 0.0 0.0 -0.00237231 0.0 0.0 0.0 2.9798 0.0 0.0 -0.00214121 0.0 0.0 0.0 3.0303 0.0 0.0 -0.00193595 0.0 0.0 0.0 3.08081 0.0 0.0 -0.00175327 0.0 0.0 0.0 3.13131 0.0 0.0 -0.00159038 0.0 0.0 0.0 3.18182 0.0 0.0 -0.00144487 0.0 0.0 0.0 3.23232 0.0 0.0 -0.00131466 0.0 0.0 0.0 3.28283 0.0 0.0 -0.00119792 0.0 0.0 0.0 3.33333 0.0 0.0 -0.0010931 0.0 0.0 0.0 3.38384 0.0 0.0 -0.000998824 0.0 0.0 0.0 3.43434 0.0 0.0 -0.000913896 0.0 0.0 0.0 3.48485 0.0 0.0 -0.000837272 0.0 0.0 0.0 3.53535 0.0 0.0 -0.000768038 0.0 0.0 0.0 3.58586 0.0 0.0 -0.000705391 0.0 0.0 0.0 3.63636 0.0 0.0 -0.000648625 0.0 0.0 0.0 3.68687 0.0 0.0 -0.000597116 0.0 0.0 0.0 3.73737 0.0 0.0 -0.000550316 0.0 0.0 0.0 3.78788 0.0 0.0 -0.00050774 0.0 0.0 0.0 3.83838 0.0 0.0 -0.000468957 0.0 0.0 0.0 3.88889 0.0 0.0 -0.000433586 0.0 0.0 0.0 3.93939 0.0 0.0 -0.000401288 0.0 0.0 0.0 3.9899 0.0 0.0 -0.000371763 0.0 0.0 0.0 4.0404 0.0 0.0 -0.000344741 0.0 0.0 0.0 4.09091 0.0 0.0 -0.000319982 0.0 0.0 0.0 4.14141 0.0 0.0 -0.000297274 0.0 0.0 0.0 4.19192 0.0 0.0 -0.000276423 0.0 0.0 0.0 4.24242 0.0 0.0 -0.000257258 0.0 0.0 0.0 4.29293 0.0 0.0 -0.000239626 0.0 0.0 0.0 4.34343 0.0 0.0 -0.000223388 0.0 0.0 0.0 4.39394 0.0 0.0 -0.000208419 0.0 0.0 0.0 4.44444 0.0 0.0 -0.000194607 0.0 0.0 0.0 4.49495 0.0 0.0 -0.000181851 0.0 0.0 0.0 4.54545 0.0 0.0 -0.00017006 0.0 0.0 0.0 4.59596 0.0 0.0 -0.000159152 0.0 0.0 0.0 4.64646 0.0 0.0 -0.000149051 0.0 0.0 0.0 4.69697 0.0 0.0 -0.00013969 0.0 0.0 0.0 4.74747 0.0 0.0 -0.000131008 0.0 0.0 0.0 4.79798 0.0 0.0 -0.000122948 0.0 0.0 0.0 4.84848 0.0 0.0 -0.000115462 0.0 0.0 0.0 4.89899 0.0 0.0 -0.000108502 0.0 0.0 0.0 4.94949 0.0 0.0 -0.000102026 0.0 0.0 0.0 5 0.0 0.0 -9.59969e-05 0.0 0.0 0.0 =================================grompp.mdp==================== ; File 'mdout.mdp' was generated ; By user: spoel (291) ; On host: chagall ; At date: Mon Dec 15 13:52:23 2003 ; ; VARIOUS PREPROCESSING OPTIONS title = Perylene ;cpp = xlc -E cpp = cpp include = define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 10000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal ;comm-mode = None comm-mode = Linear ;comm-mode = Angular ; 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-fric = 0.5 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 10 emstep = 0.01 ; Max number of iterations in relax_shells niter = 2000 ; Step size (1/ps^2) for minimization of flexible constraints 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 = 10000 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 10000 ; Output frequency for energies to log file and energy file nstlog = 10000 nstenergy = 10000 ; Output frequency and precision for xtc file nstxtcout = 100 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 = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) ;pbc = no pbc = xyz ; nblist cut-off rlist = 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.0 ; 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 = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; 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 = yes Tcoupl = Berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.01 ref_t = 300 ; Pressure coupling ;Pcoupl = Berendsen Pcoupl = no ;Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 5.0 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 = none ;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 = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 dihre-tau = 0 ; Output frequency for dihedral values to energy file nstdihreout = 100 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = E-xt = E-y = E-yt = E-z = E-zt = ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0
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