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好用的target MD 设定

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发表于 2008-7-16 15:22:00 | 显示全部楼层 |阅读模式
好用低target MD 设定
在SCRIPT中加入以下低SCRIPT COMMAND 就可以做target MD模拟[ol]
  • open read card unit 10 name top_all27_prot_na.rtf
  • read
  • rtf cardunit 10
  • open read card unit 20 namepar_all27_prot_na_gbsw.prm
  • read para card unit 20
  • ! Read PSF
  • open read unit 10 card namestep1_pdbreader.psf
  • read psf
  • unit 10 card
  • ! Read COOR
  • open read unit 10 card namestep1_pdbreader.pdb
  • read coor unit 10 pdb
  • resid
  • !open unit 1 read form name n1.crd
  • !read coor card unit 1
  • !close unit 1
  • openunit 1 read form name n3.crd
  • readcoor card compare unit 1
  • close unit 1
  • !
  • ! GBSW setup
  • !
  • prnlev 0
  • stream radii_prot_na.str
  • stream radius_gbsw.str
  • prnlev 5
  • !double check if some heavy atoms have azero radius
  • scalar wmain statistics select .not. typeH* end
  • define check select ( .not. type H* ) .and.( property wmain .eq. 0.0 ) show end
  • if ?nsel ne 0 stop
  • gbsw sgamma 0.005 nang 50
  • nbond atom switch cdie vdw vswitch ctonnb16.0 ctofnb 16.0 cutnb 20.0
  • ENERGY
  • !
  • ! short minimization and Langevin dynamics
  • ! NOTE: CHANGE ISEED EACH TIME FOR RESTARTIN LANGEVIN DYNAMICS
  • !
  • mini
  • sd nstep 50 nprint 10 step 0.005 inbfrq -1
  • !mini abnr nstep 50 nprint 10 step 0.005inbfrq -1
  • set fbeta = 5.0
  • set temp
  • = 300.0
  • scalar fbeta set @fbeta
  • scalar fbeta set 0.0
  • select type H* end
  • SHAKE BONH PARAm TOL 1.0e-6
  • set rmsd 1.20
  • open write unit 12 card name run.rst
  • open write unit 13 file name run.dcd
  • open unit 14 write form name traj.rgd
  • !rgyr force 10 reference @rmsd rmsd comporient
  • select type ca output 14 nsave100 end
  • rgyr force 100 reference @rmsd rmsd comporient
  • select .not. type H*
  • output 14 nsave 100 end
  • DYNAMICS LANGEVIN
  • start
  • nstep 10000
  • timestp 0.002
  • -
  • nprint
  • 100
  • iprfrq
  • 5000
  • isvfrq
  • 5000
  • ntrfrq
  • 500 -
  • inbfrq
  • -1
  • imgfrq
  • -1
  • ihbfrq
  • 0
  • ilbfrq
  • 0 -
  • firstt @temp
  • finalt
  • @temp
  • iseed 47858436 -
  • tbath
  • @temp
  • rbuf
  • 0.0
  • -
  • iunread
  • -1
  • iunwrite
  • 12
  • iuncrd
  • 13
  • iunvelo
  • -1 -
  • nsavcrd
  • 100
  • nsavvelo
  • 0
  • -
  • iasvel
  • 1
  • rgyr reset
  • coor orie rms select type ca end
  • open unit 1 write form name rmsd.pdb
  • write coor pdb unit 1
  • *
  • Coordiantes from frame with reference rmsd = @rmsd, current rmsd= ?rms
  • *
  • ENERGY
  • open write card unit 10 namestep2_implicit.pdb
  • write coor pdb
  • unit 10
  • stop[/ol]复制代码
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    发表于 2009-3-11 10:45:00 | 显示全部楼层
    如果用MC方法,应该怎么写?
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