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sololigando.conf

SCOTTxRT Aug 22nd, 2019 (edited) 111 Never
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  1. #############################################################
  2. ## JOB DESCRIPTION                                         ##
  3. #############################################################
  4.  
  5. # Minimization and Equilibration of
  6. # Aldosterone procesada
  7.  
  8.  
  9. #############################################################
  10. ## ADJUSTABLE PARAMETERS                                   ##
  11. #############################################################
  12.  
  13. structure          ald.psf
  14. coordinates        ald.pdb
  15.  
  16. set temperature    310
  17. set outputname     ald_wbi
  18.  
  19. firsttimestep      0
  20.  
  21.  
  22. #############################################################
  23. ## SIMULATION PARAMETERS                                   ##
  24. #############################################################
  25.  
  26. # Input
  27. paraTypeCharmm      on
  28.  
  29. parameters          ald.par
  30.  
  31.  
  32.  
  33.  
  34. temperature         $temperature
  35.  
  36.  
  37. # Force-Field Parameters
  38. exclude             scaled1-4
  39. 1-4scaling          1.0
  40. cutoff              12.0
  41. switching           on
  42. switchdist          10.0
  43. pairlistdist        14.0
  44.  
  45.  
  46. # Integrator Parameters
  47. timestep            2.0  ;# 2fs/step
  48. rigidBonds          all  ;# needed for 2fs steps
  49. nonbondedFreq       1
  50. fullElectFrequency  2  
  51. stepspercycle       10
  52.  
  53.  
  54. # Constant Temperature Control
  55. langevin            on    ;# do langevin dynamics
  56. langevinDamping     1     ;# damping coefficient (gamma) of 1/ps
  57. langevinTemp        $temperature
  58. langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
  59.  
  60.  
  61. # Periodic Boundary Conditions
  62. cellBasisVector1    42.0    0.   0.0
  63. cellBasisVector2     0.0  44.0   0.0
  64. cellBasisVector3     0.0    0   47.0
  65. cellOrigin          31.0   29.0  17.5
  66.  
  67. wrapAll             on
  68.  
  69.  
  70. # PME (for full-system periodic electrostatics)
  71. PME                 no
  72. PMEGridSpacing      5.0
  73.  
  74. #manual grid definition
  75. #PMEGridSizeX        45
  76. #PMEGridSizeY        45
  77. #PMEGridSizeZ        48
  78.  
  79.  
  80. # Constant Pressure Control (variable volume)
  81. useGroupPressure      yes ;# needed for rigidBonds
  82. useFlexibleCell       no
  83. useConstantArea       no
  84.  
  85. langevinPiston        on
  86. langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
  87. langevinPistonPeriod  100.0
  88. langevinPistonDecay   50.0
  89. langevinPistonTemp    $temperature
  90.  
  91.  
  92. # Output
  93. outputName          $outputname
  94.  
  95. restartfreq         500     ;# 500steps = every 1ps
  96. dcdfreq             250
  97. xstFreq             250
  98. outputEnergies      100
  99. outputPressure      100
  100.  
  101.  
  102. #############################################################
  103. ## EXTRA PARAMETERS                                        ##
  104. #############################################################
  105.  
  106.  
  107. #############################################################
  108. ## EXECUTION SCRIPT                                        ##
  109. #############################################################
  110.  
  111. # Minimization
  112. minimize            100
  113. reinitvels          $temperature
  114.  
  115. run 500 ;# 1ps
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