2008/8/5 Justin A. Lemkul <[EMAIL PROTECTED]>
> > 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 >> > > This would concern me a bit. You've got an enormous force on atom 5! > That's probably causing the explosion. So even though the potential energy > seems reasonable, you've got something pushing very hard against that > particle, and it may be ripping your system apart. > > You were aiming for an Fmax < 10, and got nowhere close (by a factor of a > million!) so I would check that initial configuration and examine your > parameters closely. > > -Justin > > 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 >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > Ok, Thank you very much, I will wait you reply.
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