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synthnassizer

tut2.namd

May 7th, 2015
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  1. set outputname tut2-run
  2. set temperature 310
  3. structure solvate.psf
  4. coordinates solvate.pdb
  5. paraTypeCharmm on
  6. parameters par_all27_prot_lipid_na.inp
  7. temperature $temperature
  8.  
  9. exclude scaled1-4
  10. 1-4scaling 1.0
  11. cutoff 12.0
  12. switching on
  13. switchdist 10.0
  14. pairlistdist 14.0
  15. timestep 2.0 ;# 2fs/step
  16. rigidBonds all ;# rattle algorithm
  17. nonbondedFreq 1
  18. fullElectFrequency 2
  19. stepspercycle 10
  20. langevin on ;# do langevin dynamics
  21. langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
  22. langevinTemp $temperature
  23. langevinHydrogen off ;# don't couple langevin bath to hydrogens
  24. useGroupPressure yes ;# needed for rigidBonds
  25. useFlexibleCell yes ;#useful for membrane simulations. Set to no for soluble proteins
  26. useConstantArea no
  27. langevinPiston on
  28. langevinPistonTarget 1.01325 ;# in bar -> 1 atm
  29. langevinPistonPeriod 100.0
  30. langevinPistonDecay 50.0
  31. langevinPistonTemp $temperature
  32. cellBasisVector1 61.56700000166893 0.0 0.0
  33. cellBasisVector2 0.0 62.361998319625854 0.0
  34. cellBasisVector3 0.0 0.0 66.26399803161621
  35. cellOrigin 30.821117401123047 29.162376403808594 17.781869888305664
  36. wrapAll on
  37. PME yes
  38. PMEGridSpacing 1.0
  39.  
  40. outputName $outputname
  41. restartfreq 100
  42. dcdfreq 100
  43. xstFreq 100
  44. outputEnergies 100
  45. outputPressure 100
  46.  
  47. IMDon on
  48. IMDport 3000 ;# port number (enter it in VMD)
  49. IMDfreq 1 ;# send every 1 frame
  50. IMDwait no ;# wait for VMD to connect before running?
  51. minimize 500
  52. run 10000
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