<div dir="ltr"><br><br><div class="gmail_quote">2008/8/5 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div class="Wj3C7c"><br>
<br>
Alexandr Malafeev wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Gromacs Users,<br>
<br>
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<br>
<br>
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.<br>
<br>
Can you help me?<br>
</blockquote>
<br></div></div>
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?<br>
<br>
Without knowing more about your system or the run parameters, it is difficult to give more details.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thanks in advance. <br>
<br>
------------------------------------------------------------------------<br>
<br>
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</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></blockquote><div>Yes I done energy minimization, and mdrun output here:</div>
<div></div><div>Steepest Descents converged to machine precision in 17 steps,<br>but did not reach the requested Fmax < 10.<br>Potential Energy = -1.6686725e+06<br>Maximum force = 2.4212272e+07 on atom 5<br>Norm of force = 3.4130568e+07</div>
<div></div><div>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.</div><div></div><div>==============ffgmx.itp======================== </div>
</div>[ defaults ]<br>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br> 1 1 no 1.0 1.0<br><br>[ atomtypes ]<br><br> B 337.000 0.000 A 4.275 2.14<br>
[ bondtypes ]<br>; i j func b0 kb<br> B B 1 1.3 1105.7 ; gaussian<br>[ angletypes ]<br> B B B 1 170.7 33.4<br>[ dihedraltypes ]<br> B B B B 1 164.9 0.87 1<br>
[ nonbond_params ]<br>;i j C6 C12<br> B B 1 4.275 2.14<br><br>[ pairtypes ]<br>;i j C6 C12<br> B B 1 4.275 2.14<br><p>=====================table.xvg===============================<br></p><p>0 0.0 0.0 5.31525e-317 0.0 0.0 0.0<br>
0.0505051 0.0 0.0 2.72297e 0.0 0.0 0.0<br>0.10101 0.0 0.0 6.64787e 0.0 0.0 0.0<br>0.151515 0.0 0.0 5.12363e 0.0 0.0 0.0<br>0.20202 0.0 0.0 1.6228e 0.0 0.0 0.0<br>0.252525 0.0 0.0 1.11475e 0.0 0.0 0.0<br>0.30303 0.0 0.0 1.24898e 0.0 0.0 0.0<br>
0.353535 0.0 0.0 195960 0.0 0.0 0.0<br>0.40404 0.0 0.0 39279.7 0.0 0.0 0.0<br>0.454545 0.0 0.0 9471.18 0.0 0.0 0.0<br>0.505051 0.0 0.0 2632.59 0.0 0.0 0.0<br>0.555556 0.0 0.0 816.605 0.0 0.0 0.0<br>0.606061 0.0 0.0 275.131 0.0 0.0 0.0<br>
0.656566 0.0 0.0 98.1504 0.0 0.0 0.0<br>0.707071 0.0 0.0 36.0257 0.0 0.0 0.0<br>0.757576 0.0 0.0 13.0521 0.0 0.0 0.0<br>0.808081 0.0 0.0 4.28676 0.0 0.0 0.0<br>0.858586 0.0 0.0 0.929196 0.0 0.0 0.0<br>0.909091 0.0 0.0 -0.30352 0.0 0.0 0.0<br>
0.959596 0.0 0.0 -0.690878 0.0 0.0 0.0<br>1.0101 0.0 0.0 -0.747432 0.0 0.0 0.0<br>1.06061 0.0 0.0 -0.683641 0.0 0.0 0.0<br>1.11111 0.0 0.0 -0.585339 0.0 0.0 0.0<br>1.16162 0.0 0.0 -0.486288 0.0 0.0 0.0<br>1.21212 0.0 0.0 -0.398389 0.0 0.0 0.0<br>
1.26263 0.0 0.0 -0.324521 0.0 0.0 0.0<br>1.31313 0.0 0.0 -0.264044 0.0 0.0 0.0<br>1.36364 0.0 0.0 -0.21515 0.0 0.0 0.0<br>1.41414 0.0 0.0 -0.175831 0.0 0.0 0.0<br>1.46465 0.0 0.0 -0.144252 0.0 0.0 0.0<br>1.51515 0.0 0.0 -0.118857 0.0 0.0 0.0<br>
1.56566 0.0 0.0 -0.0983815 0.0 0.0 0.0<br>1.61616 0.0 0.0 -0.0818131 0.0 0.0 0.0<br>1.66667 0.0 0.0 -0.0683514 0.0 0.0 0.0<br>1.71717 0.0 0.0 -0.0573661 0.0 0.0 0.0<br>1.76768 0.0 0.0 -0.0483612 0.0 0.0 0.0<br>1.81818 0.0 0.0 -0.0409463 0.0 0.0 0.0<br>
1.86869 0.0 0.0 -0.0348131 0.0 0.0 0.0<br>1.91919 0.0 0.0 -0.0297176 0.0 0.0 0.0<br>1.9697 0.0 0.0 -0.025466 0.0 0.0 0.0<br>2.0202 0.0 0.0 -0.0219036 0.0 0.0 0.0<br>2.07071 0.0 0.0 -0.0189067 0.0 0.0 0.0<br>2.12121 0.0 0.0 -0.0163756 0.0 0.0 0.0<br>
2.17172 0.0 0.0 -0.0142297 0.0 0.0 0.0<br>2.22222 0.0 0.0 -0.0124039 0.0 0.0 0.0<br>2.27273 0.0 0.0 -0.010845 0.0 0.0 0.0<br>2.32323 0.0 0.0 -0.00950938 0.0 0.0 0.0<br>2.37374 0.0 0.0 -0.00836141 0.0 0.0 0.0<br>2.42424 0.0 0.0 -0.00737164 0.0 0.0 0.0<br>
2.47475 0.0 0.0 -0.00651568 0.0 0.0 0.0<br>2.52525 0.0 0.0 -0.0057733 0.0 0.0 0.0<br>2.57576 0.0 0.0 -0.00512764 0.0 0.0 0.0<br>2.62626 0.0 0.0 -0.00456457 0.0 0.0 0.0<br>2.67677 0.0 0.0 -0.00407227 0.0 0.0 0.0<br>2.72727 0.0 0.0 -0.00364076 0.0 0.0 0.0<br>
2.77778 0.0 0.0 -0.00326162 0.0 0.0 0.0<br>2.82828 0.0 0.0 -0.00292772 0.0 0.0 0.0<br>2.87879 0.0 0.0 -0.002633 0.0 0.0 0.0<br>2.92929 0.0 0.0 -0.00237231 0.0 0.0 0.0<br>2.9798 0.0 0.0 -0.00214121 0.0 0.0 0.0<br>3.0303 0.0 0.0 -0.00193595 0.0 0.0 0.0<br>
3.08081 0.0 0.0 -0.00175327 0.0 0.0 0.0<br>3.13131 0.0 0.0 -0.00159038 0.0 0.0 0.0<br>3.18182 0.0 0.0 -0.00144487 0.0 0.0 0.0<br>3.23232 0.0 0.0 -0.00131466 0.0 0.0 0.0<br>3.28283 0.0 0.0 -0.00119792 0.0 0.0 0.0<br>3.33333 0.0 0.0 -0.0010931 0.0 0.0 0.0<br>
3.38384 0.0 0.0 -0.000998824 0.0 0.0 0.0<br>3.43434 0.0 0.0 -0.000913896 0.0 0.0 0.0<br>3.48485 0.0 0.0 -0.000837272 0.0 0.0 0.0<br>3.53535 0.0 0.0 -0.000768038 0.0 0.0 0.0<br>3.58586 0.0 0.0 -0.000705391 0.0 0.0 0.0<br>3.63636 0.0 0.0 -0.000648625 0.0 0.0 0.0<br>
3.68687 0.0 0.0 -0.000597116 0.0 0.0 0.0<br>3.73737 0.0 0.0 -0.000550316 0.0 0.0 0.0<br>3.78788 0.0 0.0 -0.00050774 0.0 0.0 0.0<br>3.83838 0.0 0.0 -0.000468957 0.0 0.0 0.0<br>3.88889 0.0 0.0 -0.000433586 0.0 0.0 0.0<br>3.93939 0.0 0.0 -0.000401288 0.0 0.0 0.0<br>
3.9899 0.0 0.0 -0.000371763 0.0 0.0 0.0<br>4.0404 0.0 0.0 -0.000344741 0.0 0.0 0.0<br>4.09091 0.0 0.0 -0.000319982 0.0 0.0 0.0<br>4.14141 0.0 0.0 -0.000297274 0.0 0.0 0.0<br>4.19192 0.0 0.0 -0.000276423 0.0 0.0 0.0<br>4.24242 0.0 0.0 -0.000257258 0.0 0.0 0.0<br>
4.29293 0.0 0.0 -0.000239626 0.0 0.0 0.0<br>4.34343 0.0 0.0 -0.000223388 0.0 0.0 0.0<br>4.39394 0.0 0.0 -0.000208419 0.0 0.0 0.0<br>4.44444 0.0 0.0 -0.000194607 0.0 0.0 0.0<br>4.49495 0.0 0.0 -0.000181851 0.0 0.0 0.0<br>4.54545 0.0 0.0 -0.00017006 0.0 0.0 0.0<br>
4.59596 0.0 0.0 -0.000159152 0.0 0.0 0.0<br>4.64646 0.0 0.0 -0.000149051 0.0 0.0 0.0<br>4.69697 0.0 0.0 -0.00013969 0.0 0.0 0.0<br>4.74747 0.0 0.0 -0.000131008 0.0 0.0 0.0<br>4.79798 0.0 0.0 -0.000122948 0.0 0.0 0.0<br>4.84848 0.0 0.0 -0.000115462 0.0 0.0 0.0<br>
4.89899 0.0 0.0 -0.000108502 0.0 0.0 0.0<br>4.94949 0.0 0.0 -0.000102026 0.0 0.0 0.0<br>5 0.0 0.0 -9.59969e-05 0.0 0.0 0.0<br><br>=================================grompp.mdp====================<br></p><p><br>; File 'mdout.mdp' was generated<br>
; By user: spoel (291)<br>; On host: chagall<br>; At date: Mon Dec 15 13:52:23 2003<br>;<br><br>; VARIOUS PREPROCESSING OPTIONS<br>title = Perylene<br>;cpp = xlc -E<br>
cpp = cpp<br>include =<br>define =<br><br>; RUN CONTROL PARAMETERS<br>integrator = steep<br>; Start time and timestep in ps<br>tinit = 0<br>
dt = 0.002<br>nsteps = 10000 <br>; For exact run continuation or redoing part of a run<br>init_step = 0<br>; mode for center of mass motion removal<br>;comm-mode = None<br>
comm-mode = Linear<br>;comm-mode = Angular<br>; number of steps for center of mass motion removal<br>nstcomm = 1<br>; group(s) for center of mass motion removal<br>comm-grps =<br>
<br>; LANGEVIN DYNAMICS OPTIONS<br>; Temperature, friction coefficient (amu/ps) and random seed<br>bd-fric = 0.5<br>ld-seed = 1993<br><br>; ENERGY MINIMIZATION OPTIONS<br>; Force tolerance and initial step-size<br>
emtol = 10<br>emstep = 0.01<br>; Max number of iterations in relax_shells<br>niter = 2000<br>; Step size (1/ps^2) for minimization of flexible constraints<br>fcstep = 0<br>
; Frequency of steepest descents steps when doing CG<br>nstcgsteep = 1000<br>nbfgscorr = 10<br><br>; OUTPUT CONTROL OPTIONS<br>; Output frequency for coords (x), velocities (v) and forces (f)<br>
nstxout = 10000<br>nstvout = 0<br>nstfout = 0<br>; Checkpointing helps you continue after crashes<br>nstcheckpoint = 10000<br>; Output frequency for energies to log file and energy file<br>
nstlog = 10000<br>nstenergy = 10000<br>; Output frequency and precision for xtc file<br>nstxtcout = 100<br>xtc-precision = 1000<br>; This selects the subset of atoms for the xtc file. You can<br>
; select multiple groups. By default all atoms will be written.<br>xtc-grps =<br>; Selection of energy groups<br>energygrps =<br><br>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency<br>
nstlist = 5<br>; ns algorithm (simple or grid)<br>ns_type = grid<br>; Periodic boundary conditions: xyz (default), no (vacuum)<br>; or full (infinite systems only)<br>;pbc = no<br>pbc = xyz<br>
; nblist cut-off<br>rlist = 1.0<br>domain-decomposition = no<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = Cut-off <br>rcoulomb-switch = 0<br>
rcoulomb = 1.0<br>; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>vdw-type = User<br>; cut-off lengths<br>
rvdw-switch = 0<br>rvdw = 1.0<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; Extension of the potential lookup tables beyond the cut-off<br>
table-extension = 1<br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.12<br>; FFT grid size, when a value is 0 fourierspacing will be used<br>fourier_nx = 0<br>fourier_ny = 0<br>
fourier_nz = 0<br>; EWALD/PME/PPPM parameters<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>epsilon_surface = 0<br>optimize_fft = no<br>
<br>; GENERALIZED BORN ELECTROSTATICS<br>; Algorithm for calculating Born radii<br>gb_algorithm = Still<br>; Frequency of calculating the Born radii inside rlist<br>nstgbradii = 1<br>; Cutoff for Born radii calculation; the contribution from atoms<br>
; between rlist and rgbradii is updated every nstlist steps<br>rgbradii = 2<br>; Salt concentration in M for Generalized Born models<br>gb_saltconc = 0<br><br>; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)<br>
implicit_solvent = No<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>; Temperature coupling<br>;Tcoupl = yes<br>Tcoupl = Berendsen<br>; Groups to couple separately<br>tc-grps = System<br>
; Time constant (ps) and reference temperature (K)<br>tau_t = 0.01<br>ref_t = 300<br>; Pressure coupling<br>;Pcoupl = Berendsen<br>Pcoupl = no<br>;Pcoupltype = isotropic<br>
; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>tau_p = 5.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Random seed for Andersen thermostat<br>andersen_seed = 815131<br>
<br>; SIMULATED ANNEALING<br>; Type of annealing for each temperature group (no/single/periodic)<br>annealing = no<br>; Number of time points to use for specifying annealing in each group<br>annealing_npoints =<br>
; List of times at the annealing points for each group<br>ANnealing_time =<br>; Temp. at each annealing point, for each group.<br>annealing_temp =<br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = yes<br>
gen_temp = 300<br>gen_seed = 1993<br><br>; OPTIONS FOR BONDS<br>constraints = none<br>;constraints = all-bonds<br>; Type of constraint algorithm<br>constraint-algorithm = Lincs<br>
; Do not constrain the start configuration<br>unconstrained-start = no<br>; Use successive overrelaxation to reduce the number of shake iterations<br>Shake-SOR = no<br>; Relative tolerance of shake<br>
shake-tol = 1e-04<br>; Highest order in the expansion of the constraint coupling matrix<br>lincs-order = 4<br>; Number of iterations in the final step of LINCS. 1 is fine for<br>; normal simulations, but use 2 to conserve energy in NVE runs.<br>
; For energy minimization with constraints it should be 4 to 8.<br>lincs-iter = 1<br>; Lincs will write a warning to the stderr if in one step a bond<br>; rotates over more degrees than<br>lincs-warnangle = 30<br>
; Convert harmonic bonds to morse potentials<br>morse = no<br><br>; ENERGY GROUP EXCLUSIONS<br>; Pairs of energy groups for which all non-bonded interactions are excluded<br>energygrp_excl =<br>
<br>; NMR refinement stuff<br>; Distance restraints type: No, Simple or Ensemble<br>disre = No<br>; Force weighting of pairs in one distance restraint: Conservative or Equal<br>disre-weighting = Conservative<br>
; Use sqrt of the time averaged times the instantaneous violation<br>disre-mixed = no<br>disre-fc = 1000<br>disre-tau = 0<br>; Output frequency for pair distances to energy file<br>
nstdisreout = 100<br>; Orientation restraints: No or Yes<br>orire = no<br>; Orientation restraints force constant and tau for time averaging<br>orire-fc = 0<br>orire-tau = 0<br>
orire-fitgrp =<br>; Output frequency for trace(SD) to energy file<br>nstorireout = 100<br>; Dihedral angle restraints: No, Simple or Ensemble<br>dihre = No<br>dihre-fc = 1000<br>
dihre-tau = 0<br>; Output frequency for dihedral values to energy file<br>nstdihreout = 100<br><br>; Free energy control stuff<br>free-energy = no<br>init-lambda = 0<br>
delta-lambda = 0<br>sc-alpha = 0<br>sc-sigma = 0.3<br><br>; Non-equilibrium MD stuff<br>acc-grps =<br>accelerate =<br>freezegrps =<br>
freezedim =<br>cos-acceleration = 0<br><br>; Electric fields<br>; Format is number of terms (int) and for all terms an amplitude (real)<br>; and a phase angle (real)<br>E-x =<br>
E-xt =<br>E-y =<br>E-yt =<br>E-z =<br>E-zt =<br><br>; User defined thingies<br>user1-grps =<br>user2-grps =<br>
userint1 = 0<br>userint2 = 0<br>userint3 = 0<br>userint4 = 0<br>userreal1 = 0<br>userreal2 = 0<br>userreal3 = 0<br>
userreal4 = 0<br><br><br><br></p></div>