<DIV>Dear Users, Nuno</DIV>
<DIV> </DIV>
<DIV>Sorry, I attached here my three files and seek your help to find the problem, because the Gromacs stopped when a make mdrun.</DIV>
<DIV><FONT size=2>
<P>; .gro file---------</P>
<P>Argon</P>
<P>100</P>
<P>1Argon AR 1 1.024 0.778 0.841</P>
<P>2Argon AR 2 0.067 1.713 0.853</P>
<P>3Argon AR 3 1.246 0.981 0.266</P>
<P>4Argon AR 4 0.204 0.357 0.233</P>
<P>5Argon AR 5 2.079 0.289 1.658</P>
<P>6Argon AR 6 0.962 0.295 1.403</P>
<P>7Argon AR 7 1.354 0.007 1.372</P>
<P>8Argon AR 8 1.632 1.046 0.936</P>
<P>9Argon AR 9 1.847 1.282 0.369</P>
<P>10Argon AR 10 1.930 0.924 0.641</P>
<P>11Argon AR 11 0.832 1.824 0.279</P>
<P>12Argon AR 12 1.906 1.018 1.961</P>
<P>13Argon AR 13 0.409 1.827 1.733</P>
<P>14Argon AR 14 1.695 1.810 0.181</P>
<P>15Argon AR 15 0.945 0.299 0.758</P>
<P>16Argon AR 16 0.246 0.857 1.711</P>
<P>17Argon AR 17 0.782 1.460 0.014</P>
<P>18Argon AR 18 0.556 1.150 0.250</P>
<P>19Argon AR 19 1.249 1.188 0.730</P>
<P>20Argon AR 20 1.131 1.337 1.192</P>
<P>21Argon AR 21 0.975 0.575 0.432</P>
<P>22Argon AR 22 1.908 0.095 0.363</P>
<P>23Argon AR 23 0.365 0.869 1.185</P>
<P>24Argon AR 24 1.085 1.375 0.330</P>
<P>25Argon AR 25 2.038 1.699 0.416</P>
<P>26Argon AR 26 0.081 1.315 1.745</P>
<P>27Argon AR 27 1.456 0.077 0.229</P>
<P>28Argon AR 28 0.248 0.950 0.488</P>
<P>29Argon AR 29 0.864 0.844 0.092</P>
<P>30Argon AR 30 1.383 0.182 0.675</P>
<P>31Argon AR 31 0.531 0.244 1.647</P>
<P>32Argon AR 32 1.438 1.809 0.610</P>
<P>33Argon AR 33 1.268 0.843 1.901</P>
<P>34Argon AR 34 0.578 0.153 0.363</P>
<P>35Argon AR 35 1.047 1.229 1.862</P>
<P>36Argon AR 36 0.489 1.196 1.907</P>
<P>37Argon AR 37 0.152 0.522 0.642</P>
<P>38Argon AR 38 1.874 1.381 0.881</P>
<P>39Argon AR 39 1.657 0.904 0.211</P>
<P>40Argon AR 40 1.163 2.064 1.971</P>
<P>41Argon AR 41 0.546 1.176 0.756</P>
<P>42Argon AR 42 0.131 1.097 0.903</P>
<P>43Argon AR 43 0.340 0.364 1.195</P>
<P>44Argon AR 44 0.669 2.085 2.050</P>
<P>45Argon AR 45 2.053 0.681 0.996</P>
<P>46Argon AR 46 2.079 1.664 2.032</P>
<P>47Argon AR 47 0.393 1.374 1.157</P>
<P>48Argon AR 48 1.326 0.832 1.196</P>
<P>49Argon AR 49 0.240 0.893 0.049</P>
<P>50Argon AR 50 1.040 0.101 0.359</P>
<P>51Argon AR 51 0.845 0.375 0.063</P>
<P>52Argon AR 52 0.752 2.003 0.694</P>
<P>53Argon AR 53 2.033 0.693 0.287</P>
<P>54Argon AR 54 1.137 2.010 0.976</P>
<P>55Argon AR 55 0.541 0.633 0.350</P>
<P>56Argon AR 56 2.070 0.218 0.976</P>
<P>57Argon AR 57 0.646 1.791 1.358</P>
<P>58Argon AR 58 1.793 0.084 1.971</P>
<P>59Argon AR 59 0.761 0.545 1.095</P>
<P>60Argon AR 60 0.173 0.056 0.616</P>
<P>61Argon AR 61 1.429 0.653 0.765</P>
<P>62Argon AR 62 0.706 1.490 0.527</P>
<P>63Argon AR 63 0.563 0.629 1.478</P>
<P>64Argon AR 64 0.204 1.387 0.571</P>
<P>65Argon AR 65 0.728 0.074 1.121</P>
<P>66Argon AR 66 0.870 1.007 0.512</P>
<P>67Argon AR 67 1.901 1.857 1.186</P>
<P>68Argon AR 68 2.091 0.564 1.980</P>
<P>69Argon AR 69 0.620 1.667 0.938</P>
<P>70Argon AR 70 0.611 1.171 1.486</P>
<P>71Argon AR 71 1.766 0.863 1.361</P>
<P>72Argon AR 72 1.660 0.616 1.823</P>
<P>73Argon AR 73 0.993 0.478 1.774</P>
<P>74Argon AR 74 1.784 2.040 0.765</P>
<P>75Argon AR 75 0.395 1.791 0.510</P>
<P>76Argon AR 76 1.263 1.733 0.164</P>
<P>77Argon AR 77 0.044 0.628 1.411</P>
<P>78Argon AR 78 0.866 2.041 1.649</P>
<P>79Argon AR 79 1.228 0.392 1.086</P>
<P>80Argon AR 80 1.392 0.556 0.353</P>
<P>81Argon AR 81 0.505 0.301 0.782</P>
<P>82Argon AR 82 0.973 0.814 1.430</P>
<P>83Argon AR 83 0.215 2.089 1.417</P>
<P>84Argon AR 84 1.801 0.442 0.631</P>
<P>85Argon AR 85 0.165 2.011 0.196</P>
<P>86Argon AR 86 2.015 1.919 1.688</P>
<P>87Argon AR 87 0.529 0.743 0.782</P>
<P>88Argon AR 88 1.064 1.619 0.761</P>
<P>89Argon AR 89 0.787 1.054 1.092</P>
<P>90Argon AR 90 1.313 0.397 2.048</P>
<P>91Argon AR 91 1.817 0.157 1.361</P>
<P>92Argon AR 92 0.019 1.173 1.332</P>
<P>93Argon AR 93 1.663 0.436 1.074</P>
<P>94Argon AR 94 0.474 0.549 1.992</P>
<P>95Argon AR 95 0.333 2.018 1.008</P>
<P>96Argon AR 96 0.742 0.864 1.809</P>
<P>97Argon AR 97 0.245 0.130 1.950</P>
<P>98Argon AR 98 0.428 1.701 0.055</P>
<P>99Argon AR 99 1.736 0.426 0.139</P>
<P>100Argon AR 100 0.149 1.315 0.130</P>
<P>5.10000 5.10000 5.10000</P></FONT></DIV>
<DIV> </DIV>
<DIV>; ------- .top file</DIV>
<DIV> <FONT size=2></DIV>
<P>; Argon</P>
<P>[ defaults ]</P>
<P>; nb-function combinationrule</P>
<P>1 2</P>
<P>[ atomtypes ]</P>
<P>; type mass charge ptype sig eps</P>
<P>AR 1.0 0.0 A 1.0 1.0 </P>
<P>[ moleculetype ]</P>
<P>; molname nrexcl</P>
<P>Argon 1</P>
<P>[ atoms ]</P>
<P>; id at type res nr residu name at name cg nr</P>
<P>1 AR 1 Argon AR 1 </P>
<P>[ system ]</P>
<P>; systemname</P>
<P>Argon</P>
<P>[ molecules ]</P>
<P>; molecule number</P>
<P>Argon 100</P>
<P></FONT> </P>
<DIV> </DIV>
<DIV>;-----mdp file </DIV>
<DIV> </DIV>
<DIV><FONT size=2>
<P>; VARIOUS PREPROCESSING OPTIONS</P>
<P>;title = Yo</P>
<P>;cpp = /lib/cpp</P>
<P>title = Albert-md</P>
<P>cpp = c:\Progra~1\Gromacs\bin\cpp.exe</P>
<P>include = </P>
<P>define = </P>
<P>;</P>
<P>; RUN CONTROL PARAMETERS</P>
<P>integrator = md</P>
<P>; start time and timestep in ps</P>
<P>tinit = 0.0</P>
<P>dt = 0.002</P>
<P>nsteps = 1000</P>
<P>; after checkpoint or tpbconv restart we can start on step > 0</P>
<P>;init_step = 0 ; ????</P>
<P>; mode for center of mass motion removal</P>
<P>comm-mode = Linear</P>
<P>; number of steps for center of mass motion removal</P>
<P>nstcomm = 1</P>
<P>; group(s) for center of mass motion removal</P>
<P>comm-grps = </P>
<P>;</P>
<P>; LANGEVIN DYNAMICS OPTIONS</P>
<P>; Temperature, friction coefficient (amu/ps) and random seed</P>
<P>bd-temp = 300</P>
<P>bd-fric = 0</P>
<P>ld_seed = 1993</P>
<P>;</P>
<P>; ENERGY MINIMIZATION OPTIONS</P>
<P>; Force tolerance and initial step-size</P>
<P>emtol = 0.001</P>
<P>emstep = 0.1</P>
<P>; Max number of iterations in relax_shells</P>
<P>niter = 100</P>
<P>; Step size (1/ps^2) for minimization of flexible constraints</P>
<P>fcstep = 0</P>
<P>; Frequency of steepest descents steps when doing CG</P>
<P>nstcgsteep = 1000</P>
<P>;</P>
<P>; OUTPUT CONTROL OPTIONS</P>
<P>; Output frequency for coords (x), velocities (v) and forces (f)</P>
<P>nstxout = 10</P>
<P>nstvout = 10</P>
<P>nstfout = 0</P>
<P>; Checkpointing helps you continue after crashes</P>
<P>;nstcheckpoint = 1000 ;????</P>
<P>; Output frequency for energies to log file and energy file</P>
<P>nstlog = 0</P>
<P>nstenergy = 1</P>
<P>; Output frequency and precision for xtc file</P>
<P>nstxtcout = 0</P>
<P>xtc_precision = 1000</P>
<P>; This selects the subset of atoms for the xtc file. You can</P>
<P>; select multiple groups. By default all atoms will be written.</P>
<P>xtc-grps = </P>
<P>; Selection of energy groups</P>
<P>energygrps = Argon</P>
<P>;</P>
<P>; NEIGHBORSEARCHING PARAMETERS</P>
<P>; nblist update frequency</P>
<P>nstlist = 1</P>
<P>; ns algorithm (simple or grid)</P>
<P>ns_type = simple</P>
<P>; Periodic boundary conditions: xyz or no</P>
<P>pbc = xyz</P>
<P>; nblist cut-off </P>
<P>rlist = 2.5</P>
<P>;domain-decomposition = no ;???????</P>
<P>;</P>
<P>; OPTIONS FOR ELECTROSTATICS AND VDW</P>
<P>; Method for doing electrostatics</P>
<P>coulombtype = Cut-off</P>
<P>rcoulomb_switch = 0 ;???? original -</P>
<P>rcoulomb = 2.5</P>
<P>; Dielectric constant (DC) for cut-off or DC of reaction field</P>
<P>epsilon_r = 1</P>
<P>; Method for doing Van der Waals</P>
<P>vdw-type = Cut-off</P>
<P>; cut-off lengths </P>
<P>rvdw_switch = 0 ; ????? original -</P>
<P>rvdw = 2.5</P>
<P>; Apply long range dispersion corrections for Energy and Pressure</P>
<P>DispCorr = No</P>
<P>; Spacing for the PME/PPPM FFT grid</P>
<P>fourierspacing = 0.12</P>
<P>; FFT grid size, when a value is 0 fourierspacing will be used</P>
<P>fourier_nx = 10</P>
<P>fourier_ny = 10</P>
<P>fourier_nz = 10</P>
<P>; EWALD/PME/PPPM parameters</P>
<P>pme_order = 4</P>
<P>ewald_rtol = 1e-05</P>
<P>ewald_geometry = 3d</P>
<P>surface_epsilon = 0 ;?????? original: epsilon_surface </P>
<P>optimize_fft = no</P>
<P>;</P>
<P>; GENERALIZED BORN ELECTROSTATICS</P>
<P>; Algorithm for calculating Born radii</P>
<P>;gb_algorithm = Still ;????</P>
<P>; Frequency of calculating the Born radii inside rlist</P>
<P>;nstgbradii = 1 ;????</P>
<P>; Cutoff for Born radii calculation; the contribution from atoms</P>
<P>; between rlist and rgbradii is updated every nstlist steps</P>
<P>;rgbradii = 2 ;????</P>
<P>; Salt concentration in M for Generalized Born models</P>
<P>;gb_saltconc = 0 ;??????</P>
<P>;</P>
<P>; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)</P>
<P>;implicit_solvent = No ;???????</P>
<P>;</P>
<P>; OPTIONS FOR WEAK COUPLING ALGORITHMS</P>
<P>; Temperature coupling </P>
<P>tcoupl = no</P>
<P>; Groups to couple separately</P>
<P>tc-grps = Argon</P>
<P>; Time constant (ps) and reference temperature (K)</P>
<P>tau_t = 0.1</P>
<P>ref_t = 120</P>
<P>; Pressure coupling </P>
<P>Pcoupl = no</P>
<P>Pcoupltype = Isotropic</P>
<P>; Time constant (ps), compressibility (1/bar) and reference P (bar)</P>
<P>tau_p = 1.0</P>
<P>compressibility = </P>
<P>ref_p = 1.0</P>
<P>; Random seed for Andersen thermostat</P>
<P>;andersen_seed = 815131 ;?????</P>
<P>;</P>
<P>; SIMULATED ANNEALING </P>
<P>; Type of annealing for each temperature group (no/single/periodic)</P>
<P>annealing = no</P>
<P>; Number of time points to use for specifying annealing in each group</P>
<P>annealing_npoints = </P>
<P>; List of times at the annealing points for each group</P>
<P>annealing_time = </P>
<P>; Temp. at each annealing point, for each group.</P>
<P>annealing_temp = </P>
<P>; GENERATE VELOCITIES FOR STARTUP RUN</P>
<P>gen_vel = no</P>
<P>gen_temp = 120</P>
<P>gen_seed = 173529</P>
<P>; OPTIONS FOR BONDS </P>
<P>constraints = none</P>
<P>; Type of constraint algorithm</P>
<P>constraint_algorithm = Lincs</P>
<P>; Do not constrain the start configuration</P>
<P>unconstrained_start = no</P>
<P>; Use successive overrelaxation to reduce the number of shake iterations</P>
<P>Shake-SOR = no</P>
<P>; Relative tolerance of shake</P>
<P>shake_tol = 0.0001</P>
<P>; Highest order in the expansion of the constraint coupling matrix</P>
<P>lincs_order = 4</P>
<P>; Number of iterations in the final step of LINCS. 1 is fine for</P>
<P>; normal simulations, but use 2 to conserve energy in NVE runs.</P>
<P>; For energy minimization with constraints it should be 4 to 8.</P>
<P>lincs-iter = 1 ;?????</P>
<P>; Lincs will write a warning to the stderr if in one step a bond</P>
<P>; rotates over more degrees than</P>
<P>lincs_warnangle = 30</P>
<P>; Convert harmonic bonds to morse potentials</P>
<P>morse = no</P>
<P>; ENERGY GROUP EXCLUSIONS</P>
<P>; Pairs of energy groups for which all non-bonded interactions are excluded</P>
<P>energygrp_excl = </P>
<P>; NMR refinement stuff </P>
<P>; Distance restraints type: No, Simple or Ensemble</P>
<P>disre = No</P>
<P>; Force weighting of pairs in one distance restraint: Conservative or Equal</P>
<P>disre_weighting = Equal</P>
<P>; Use sqrt of the time averaged times the instantaneous violation</P>
<P>disre_mixed = no</P>
<P>disre_fc = 1000</P>
<P>disre_tau = 1.25</P>
<P>; Output frequency for pair distances to energy file</P>
<P>nstdisreout = 100</P>
<P>; Orientation restraints: No or Yes</P>
<P>orire = no</P>
<P>; Orientation restraints force constant and tau for time averaging</P>
<P>orire-fc = 0</P>
<P>orire-tau = 0</P>
<P>orire-fitgrp = </P>
<P>; Output frequency for trace(SD) to energy file</P>
<P>nstorireout = 100</P>
<P>; Dihedral angle restraints: No, Simple or Ensemble</P>
<P>;dihre = No ;??????</P>
<P>;dihre-fc = 1000 ;?????</P>
<P>;dihre-tau = 0</P>
<P>; Output frequency for dihedral values to energy file</P>
<P>;nstdihreout = 100 ;????? </P>
<P>; Free energy control stuff</P>
<P>free_energy = no</P>
<P>init_lambda = 0</P>
<P>delta_lambda = 0</P>
<P>sc-alpha = 0</P>
<P>sc-sigma = 0.3</P>
<P>; Non-equilibrium MD stuff</P>
<P>acc-grps = </P>
<P>accelerate = </P>
<P>freezegrps = </P>
<P>freezedim = </P>
<P>cos-acceleration = 0</P>
<P>; Electric fields </P>
<P>; Format is number of terms (int) and for all terms an amplitude (real)</P>
<P>; and a phase angle (real)</P>
<P>E-x = </P>
<P>E-xt = </P>
<P>E-y = </P>
<P>E-yt = </P>
<P>E-z = </P>
<P>E-zt = </P>
<P>; User defined thingies</P>
<P>user1-grps = </P>
<P>user2-grps = </P>
<P>userint1 = 0</P>
<P>userint2 = 0</P>
<P>userint3 = 0</P>
<P>userint4 = 0</P>
<P>userreal1 = 0</P>
<P>userreal2 = 0</P>
<P>userreal3 = 0</P>
<P>userreal4 = 0</P></FONT></DIV>
<DIV> </DIV>
<DIV>Many Thanks</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Albert</DIV>
<DIV> <BR><BR><B><I>"Nuno R. L. Ferreira" <nunolf@ci.uc.pt></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">I'm so sorry gmx's, but sometimes I can't see the attachs.(tranfer encoded<BR>by smth)<BR>Why don't you send it as plain text?<BR><BR>BTW, a silly question. When I reply to someone, I was never able to put my<BR>answer just below the question tree in the gmx mail-list. Usually I do a<BR>reply to the gmx-digest e-mail, discarting all the messages except the one<BR>to reply for. Then, just change the subject to the question posed.<BR><BR>At・<BR>Nuno<BR><BR><BR>#######################################<BR>Nuno Ricardo Santos Loureiro da Silva Ferreira<BR>Departamento de Qu匇ica<BR>Faculdade de Ci麩cias e Tecnologia<BR>Universidade de Coimbra<BR>3004-535 Coimbra - Portugal<BR>Fax: +351 239 827703 - www.biolchem.qui.uc.pt<BR>#######################################<BR><BR><BR>_______________________________________________<BR>gmx-users mailing
list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.</BLOCKQUOTE><p><hr SIZE=1>
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