G2A Many GEOs
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  1. Command line:
  2.   gmx grompp -f em.mdp -c water.pdb -p newtop.top
  3.  
  4.  
  5. Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
  6. Setting the LD random seed to 2148093003
  7. Generated 5253 of the 5253 non-bonded parameter combinations
  8. Generating 1-4 interactions: fudge = 0.5
  9. Generated 5253 of the 5253 1-4 parameter combinations
  10. Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
  11. Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
  12. Excluding 2 bonded neighbours molecule type 'SOL'
  13. Excluding 2 bonded neighbours molecule type 'SOL'
  14. Excluding 2 bonded neighbours molecule type 'SOL'
  15. Excluding 2 bonded neighbours molecule type 'SOL'
  16. Excluding 2 bonded neighbours molecule type 'SOL'
  17. Excluding 2 bonded neighbours molecule type 'SOL'
  18. Excluding 2 bonded neighbours molecule type 'SOL'
  19. Excluding 2 bonded neighbours molecule type 'SOL'
  20. Excluding 2 bonded neighbours molecule type 'SOL'
  21. Excluding 2 bonded neighbours molecule type 'SOL'
  22. Excluding 2 bonded neighbours molecule type 'SOL'
  23. Excluding 2 bonded neighbours molecule type 'SOL'
  24. Excluding 2 bonded neighbours molecule type 'SOL'
  25. Excluding 2 bonded neighbours molecule type 'SOL'
  26. Excluding 2 bonded neighbours molecule type 'SOL'
  27. Excluding 2 bonded neighbours molecule type 'SOL'
  28. Excluding 2 bonded neighbours molecule type 'SOL'
  29. Excluding 2 bonded neighbours molecule type 'SOL'
  30. Excluding 2 bonded neighbours molecule type 'SOL'
  31. Excluding 2 bonded neighbours molecule type 'SOL'
  32. Excluding 2 bonded neighbours molecule type 'SOL'
  33. Excluding 2 bonded neighbours molecule type 'SOL'
  34. Excluding 2 bonded neighbours molecule type 'SOL'
  35. Excluding 2 bonded neighbours molecule type 'SOL'
  36. Excluding 2 bonded neighbours molecule type 'SOL'
  37. Excluding 2 bonded neighbours molecule type 'SOL'
  38. Excluding 2 bonded neighbours molecule type 'SOL'
  39. Excluding 2 bonded neighbours molecule type 'SOL'
  40. Excluding 2 bonded neighbours molecule type 'SOL'
  41. Excluding 2 bonded neighbours molecule type 'SOL'
  42. Excluding 2 bonded neighbours molecule type 'SOL'
  43. Excluding 2 bonded neighbours molecule type 'SOL'
  44. Excluding 2 bonded neighbours molecule type 'SOL'
  45. Excluding 2 bonded neighbours molecule type 'SOL'
  46. Excluding 2 bonded neighbours molecule type 'SOL'
  47. Excluding 2 bonded neighbours molecule type 'SOL'
  48. Excluding 2 bonded neighbours molecule type 'SOL'
  49. Excluding 2 bonded neighbours molecule type 'SOL'
  50. Excluding 2 bonded neighbours molecule type 'SOL'
  51. Excluding 2 bonded neighbours molecule type 'SOL'
  52. Excluding 2 bonded neighbours molecule type 'SOL'
  53.  
  54. NOTE 1 [file newtop.top, line 55]:
  55.   System has non-zero total charge: -3.000000
  56.   Total charge should normally be an integer. See
  57.   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  58.   for discussion on how close it should be to an integer.
  59.  
  60.  
  61.  
  62. Removing all charge groups because cutoff-scheme=Verlet
  63. Analysing residue names:
  64. There are:   116    Protein residues
  65. There are:  9025      Water residues
  66. Analysing Protein...
  67. Number of degrees of freedom in T-Coupling group rest is 86868.00
  68. Calculating fourier grid dimensions for X Y Z
  69. Using a fourier grid of 60x60x60, spacing 0.119 0.119 0.119
  70. Estimate for the relative computational load of the PME mesh part: 0.16
  71. This run will generate roughly 2 Mb of data
  72.  
  73. There was 1 note
  74.  
  75. Back Off! I just backed up topol.tpr to ./#topol.tpr.3#
  76.  
  77. gcq#516: "In practice, throwing traditional norms and values overboard results not in perfect freedom and relationships based on reason, but in chaos and fear" (Paul Verhaeghe)
  78.  
  79. maiia@SpectrumAnalayzer:~/Рабочий стол/Protein$
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