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thesketh

AdAA conf file

Nov 5th, 2018
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  1. #############################################################
  2. ## JOB DESCRIPTION ##
  3. #############################################################
  4.  
  5. # Minimization and equilibration of
  6. # ['A', 'dA', 'A'] in a 15 angstrom water box
  7.  
  8. #############################################################
  9. ## ADJUSTABLE PARAMETERS ##
  10. #############################################################
  11.  
  12. structure AdAA_wb.psf
  13. coordinates AdAA_wb.pdb
  14.  
  15. # Periodic boundary conditions - saved in separate file.
  16. cellBasisVector1 40.277000427246094 0 0
  17. cellBasisVector2 0 34.85300064086914 0
  18. cellBasisVector3 0 0 34.757999420166016
  19. cellOrigin 0.29497894644737244 0.5287485122680664 0.13249140977859497
  20.  
  21. firsttimestep 0
  22.  
  23. set outputname AdAA
  24.  
  25. #############################################################
  26. ## SIMULATION PARAMETERS ##
  27. #############################################################
  28.  
  29. # Input
  30. paraTypeCharmm on
  31. parameters /users/travis/.charmm/par_all36_prot.prm
  32. parameters /users/travis/.charmm/par_all36_carb.prm
  33. parameters /users/travis/.charmm/par_all36_lipid.prm
  34. parameters /users/travis/.charmm/par_all35_ethers.prm
  35. parameters /users/travis/.charmm/par_all36_na.prm
  36. parameters /users/travis/.charmm/par_all36_cgenff.prm
  37. parameters /users/travis/.charmm/toppar_water_ions_namd.str
  38. parameters /users/travis/.charmm/toppar_all36_prot_c36_d_aminoacids.str
  39.  
  40. # Force-Field Parameters
  41. margin 2
  42. exclude scaled1-4
  43. 1-4scaling 1.0
  44. cutoff 12.0
  45. switching on
  46. switchdist 10.0
  47. pairlistdist 14.0
  48.  
  49.  
  50. # Integrator Parameters
  51. timestep 2.0 ;# 2fs/step
  52. rigidBonds all ;# needed for 2fs steps
  53. nonbondedFreq 1
  54. fullElectFrequency 2
  55. stepspercycle 10
  56.  
  57.  
  58. # Constant Temperature Control
  59. langevin on ;# do langevin dynamics
  60. langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
  61. langevinHydrogen off ;# don't couple langevin bath to hydrogens
  62.  
  63. wrapAll on
  64.  
  65. # Constant Pressure Control (variable volume)
  66. useGroupPressure yes ;# needed for rigidBonds
  67. useFlexibleCell no
  68. useConstantArea no
  69.  
  70. langevinPiston on
  71. langevinPistonTarget 1.01325 ;# in bar -> 1 atm
  72. langevinPistonPeriod 100.0
  73. langevinPistonDecay 50.0
  74.  
  75. # Output
  76. outputName $outputname
  77.  
  78. restartfreq 100 ;# 100steps = every 200fs
  79. file mkdir $outputname
  80. dcdfreq 2000
  81. outputEnergies 5000
  82. outputPressure 5000
  83.  
  84. #############################################################
  85. ## EXECUTION SCRIPT ##
  86. #############################################################
  87.  
  88. # Minimization
  89.  
  90. temperature 298
  91. set temperature 298
  92. langevinTemp $temperature
  93. langevinPistonTemp $temperature
  94.  
  95. minimize 500
  96.  
  97. run 5000000 ;# 10ns
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